Почему авторизация через .htaccess не работает в некоторых папках?

ErrorDocument 404 /ecodes/404.html
ErrorDocument 403 /ecodes/403.html
ErrorDocument 401 /ecodes/401.html
ErrorDocument 500 /ecodes/500.html

SetEnvIf Request_URI "p/*.*" REDIRECT_noauth=1

Options -Indexes

AuthType Basic
AuthName "Please login, this area is protected!"
AuthUserFile /var/www/server.domian.ru/invent/.htpasswd
Order Deny,Allow
Satisfy any
Deny from all
Allow from env=REDIRECT_noauth
require valid-user

<FilesMatch  "\.(pl_|pm|cookie)$">
Order Deny,Allow
Deny from all
</FilesMatch>

<VirtualHost *:80>
	ServerAdmin beklemishev@domain.ru

	DocumentRoot /var/www/server.domain.ru
	ServerName server.domain.ru
#	<Directory />
#		Options FollowSymLinks
#		AllowOverride None
#	</Directory>
	<Directory /var/www/server.domain.ru/>
		Options Indexes FollowSymLinks MultiViews
		AllowOverride All
		Order allow,deny
		allow from all
	</Directory>
	
	#ScriptAlias /cgi-bin/ /home/www/cgi-bin/
	Alias /cgi-bin /home/www/cgi-bin
	<Directory "/home/www/cgi-bin">
		AllowOverride All
		#AllowOverride AuthConfig 
		#Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
		AddHandler cgi-script cgi pl
		Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
		#Option +ExecCGI
		#Order allow,deny
		#Allow from all
#		Require all granted
	</Directory>
#	<Directory "/home/www/cgi-bin/skd/api/">
#		AllowOverride All
#	</Directory>

	ErrorLog ${APACHE_LOG_DIR}/error.server.domain.ru.log

	# Possible values include: debug, info, notice, warn, error, crit,
	# alert, emerg.
	LogLevel debug

	CustomLog ${APACHE_LOG_DIR}/access.server.domain.ru.log combined
</VirtualHost>

<VirtualHost *:80>
	ServerAdmin beklemishev@domain.ru

	DocumentRoot /var/www/weather.domain.ru
	ServerName weather.domain.ru
#	<Directory />
#		Options FollowSymLinks
#		AllowOverride None
#	</Directory>
	<Directory /var/www/weather.domain.ru/>
		Options Indexes FollowSymLinks MultiViews
		AllowOverride All
		Order allow,deny
		allow from all
	</Directory>

	Alias /api /home/www/cgi-bin/p/temperature/api
	<Directory "/home/www/cgi-bin/p/temperature/api">
		AllowOverride All
#		AuthType None
		AddHandler cgi-script cgi pl
		Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
		#Order allow,deny
		#Allow from all
		Require all granted
	</Directory>

	ErrorLog ${APACHE_LOG_DIR}/error.weather.domain.ru.log

	# Possible values include: debug, info, notice, warn, error, crit,
	# alert, emerg.
	LogLevel warn

	CustomLog ${APACHE_LOG_DIR}/access.weather.domain.ru.log combined
</VirtualHost>

# This is the main Apache server configuration file.  It contains the
# configuration directives that give the server its instructions.
# See http://httpd.apache.org/docs/2.2/ for detailed information about
# the directives and /usr/share/doc/apache2-common/README.Debian.gz about
# Debian specific hints.
#
#
# Summary of how the Apache 2 configuration works in Debian:
# The Apache 2 web server configuration in Debian is quite different to
# upstream's suggested way to configure the web server. This is because Debian's
# default Apache2 installation attempts to make adding and removing modules,
# virtual hosts, and extra configuration directives as flexible as possible, in
# order to make automating the changes and administering the server as easy as
# possible.

# It is split into several files forming the configuration hierarchy outlined
# below, all located in the /etc/apache2/ directory:
#
#	/etc/apache2/
#	|-- apache2.conf
#	|	`--  ports.conf
#	|-- mods-enabled
#	|	|-- *.load
#	|	`-- *.conf
#	|-- conf.d
#	|	`-- *
# 	`-- sites-enabled
#	 	`-- *
#
#
# * apache2.conf is the main configuration file (this file). It puts the pieces
#   together by including all remaining configuration files when starting up the
#   web server.
#
#   In order to avoid conflicts with backup files, the Include directive is
#   adapted to ignore files that:
#   - do not begin with a letter or number
#   - contain a character that is neither letter nor number nor _-:.
#   - contain .dpkg
#
#   Yet we strongly suggest that all configuration files either end with a
#   .conf or .load suffix in the file name. The next Debian release will
#   ignore files not ending with .conf (or .load for mods-enabled).
#
# * ports.conf is always included from the main configuration file. It is
#   supposed to determine listening ports for incoming connections, and which
#   of these ports are used for name based virtual hosts.
#
# * Configuration files in the mods-enabled/ and sites-enabled/ directories
#   contain particular configuration snippets which manage modules or virtual
#   host configurations, respectively.
#
#   They are activated by symlinking available configuration files from their
#   respective *-available/ counterparts. These should be managed by using our
#   helpers a2enmod/a2dismod, a2ensite/a2dissite. See
#   their respective man pages for detailed information.
#
# * Configuration files in the conf.d directory are either provided by other
#   packages or may be added by the local administrator. Local additions
#   should start with local- or end with .local.conf to avoid name clashes. All
#   files in conf.d are considered (excluding the exceptions noted above) by
#   the Apache 2 web server.
#
# * The binary is called apache2. Due to the use of environment variables, in
#   the default configuration, apache2 needs to be started/stopped with
#   /etc/init.d/apache2 or apache2ctl. Calling /usr/bin/apache2 directly will not
#   work with the default configuration.


# Global configuration
#

#
# ServerRoot: The top of the directory tree under which the server's
# configuration, error, and log files are kept.
#
# NOTE!  If you intend to place this on an NFS (or otherwise network)
# mounted filesystem then please read the LockFile documentation (available
# at <URL:http://httpd.apache.org/docs/2.2/mod/mpm_common.html#lockfile>);
# you will save yourself a lot of trouble.
#
# Do NOT add a slash at the end of the directory path.
#
#ServerRoot "/etc/apache2"

#
# The accept serialization lock file MUST BE STORED ON A LOCAL DISK.
#
LockFile ${APACHE_LOCK_DIR}/accept.lock

#
# PidFile: The file in which the server should record its process
# identification number when it starts.
# This needs to be set in /etc/apache2/envvars
#
PidFile ${APACHE_PID_FILE}

#
# Timeout: The number of seconds before receives and sends time out.
#
Timeout 300
#LoadModule cgi_module modules/mod_cgi.so
#
# KeepAlive: Whether or not to allow persistent connections (more than
# one request per connection). Set to "Off" to deactivate.
#
KeepAlive On

#
# MaxKeepAliveRequests: The maximum number of requests to allow
# during a persistent connection. Set to 0 to allow an unlimited amount.
# We recommend you leave this number high, for maximum performance.
#
MaxKeepAliveRequests 100

#
# KeepAliveTimeout: Number of seconds to wait for the next request from the
# same client on the same connection.
#
KeepAliveTimeout 5

##
## Server-Pool Size Regulation (MPM specific)
## 

<IfModule mpm_prefork_module>
    StartServers          5
    MinSpareServers       5
    MaxSpareServers      10
    MaxClients          150
    MaxRequestsPerChild   0
</IfModule>

<IfModule mpm_worker_module>
    StartServers          2
    MinSpareThreads      25
    MaxSpareThreads      75 
    ThreadLimit          64
    ThreadsPerChild      25
    MaxClients          150
    MaxRequestsPerChild   0
</IfModule>

<IfModule mpm_event_module>
    StartServers          2
    MinSpareThreads      25
    MaxSpareThreads      75 
    ThreadLimit          64
    ThreadsPerChild      25
    MaxClients          150
    MaxRequestsPerChild   0
</IfModule>

# These need to be set in /etc/apache2/envvars
User ${APACHE_RUN_USER}
Group ${APACHE_RUN_GROUP}

#
# AccessFileName: The name of the file to look for in each directory
# for additional configuration directives.  See also the AllowOverride
# directive.
#

AccessFileName .htaccess

#
# The following lines prevent .htaccess and .htpasswd files from being 
# viewed by Web clients. 
#
<Files ~ "^\.ht">
    Order allow,deny
    Deny from all
    Satisfy all
</Files>

#--------------------------------------------------------------------------------------
#<Directory /var/www/>
#	Options Indexes FollowSymLinks
#	AllowOverride All
#	Require all granted
#</Directory>

DefaultType None

HostnameLookups Off

ErrorLog ${APACHE_LOG_DIR}/error.log

LogLevel debug

# Include module configuration:
Include mods-enabled/*.load
Include mods-enabled/*.conf

# Include list of ports to listen on and which to use for name based vhosts
Include ports.conf

#
# The following directives define some format nicknames for use with
# a CustomLog directive (see below).
# If you are behind a reverse proxy, you might want to change %h into %{X-Forwarded-For}i
#
LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_combined
LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined
LogFormat "%h %l %u %t \"%r\" %>s %O" common
LogFormat "%{Referer}i -> %U" referer
LogFormat "%{User-agent}i" agent

# Include of directories ignores editors' and dpkg's backup files,
# see the comments above for details.

# Include generic snippets of statements
Include conf.d/

# Include the virtual host configurations:
Include sites-enabled/
AddDefaultCharset UTF-8