This bug has been fixed in CVS.

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I rebuilt PHP from the CVS, snapshot http://snaps.php.net/php5.3-200903271530.tar.bz2 (latest snapshot currently available). The issue remains, all php.ini-entries are ignored silently when using the apache2 SAPI.

Oddly enough, the CLI SAPI works fine and reads the config file as expected.

Here's my configure line:
'./configure' '--prefix=/usr/lib64/php5' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/lib64/php5/man' '--infodir=/usr/lib64/php5/info' '--sysconfdir=/etc' '--cache-file=./config.cache' '--with-libdir=lib64' '--disable-cli' '--with-apxs2=/usr/sbin/apxs2' '--disable-cgi' '--with-config-file-path=/etc/php/apache2-php5' '--with-config-file-scan-dir=/etc/php/apache2-php5/ext-active' '--without-pear' '--disable-bcmath' '--with-bz2' '--disable-calendar' '--with-curl' '--without-curlwrappers' '--disable-dbase' '--disable-exif' '--without-fbsql' '--disable-fileinfo' '--enable-ftp' '--with-gettext' '--with-gmp' '--disable-hash' '--without-kerberos' '--enable-mbstring' '--with-mcrypt' '--without-mhash' '--without-msql' '--without-mssql' '--with-openssl' '--with-openssl-dir=/usr' '--disable-pcntl' '--with-pgsql' '--disable-posix' '--with-pspell' '--without-recode' '--disable-simplexml' '--disable-shmop' '--with-snmp' '--enable-soap' '--disable-sockets' '--without-sybase-ct' '--disable-sysvmsg' '--disable-sysvsem' '--disable-sysvshm' '--with-tidy' '--enable-wddx' '--disable-xmlreader' '--disable-xmlwriter' '--with-xmlrpc' '--with-xsl' '--enable-zip' '--with-zlib' '--disable-debug' '--enable-dba' '--without-cdb' '--with-db4' '--disable-flatfile' '--with-gdbm' '--disable-inifile' '--without-qdbm' '--with-freetype-dir=/usr' '--with-t1lib=/usr' '--disable-gd-jis-conv' '--with-jpeg-dir=/usr' '--with-png-dir=/usr' '--with-xpm-dir=/usr' '--with-gd' '--with-imap' '--with-imap-ssl' '--with-mysql=/usr' '--with-mysql-sock=/var/run/mysqld/mysqld.sock' '--with-mysqli=/usr/bin/mysql_config' '--without-pdo-dblib' '--with-pdo-mysql=/usr' '--without-pdo-odbc' '--with-pdo-pgsql' '--with-pdo-sqlite=/usr' '--with-readline' '--without-libedit' '--without-mm' '--with-sqlite=/usr' '--enable-sqlite-utf8' '--with-sqlite3'

I just ran apache with strace to make sure that the php.ini file is actually opened. It is opened, but I'm not sure how to debug if the values are getting parsed and probably overwritten later or if the values in the php.ini file are silently ignored.

What exactly is in that file?

It is the stock php.ini-development file, where I tried to set the default timezone to "Europe/Berlin". As it didn't work, I reverted my change of the timezone and tried modifying other values, for example, the error reporting and also simple values like "precision". None of my changes were shown after a restart of apache using the phpinfo()-call.

As I said before, changes are accepted when using the cli sapi.

To make this a bit simpler, delete that file and create one with only 
this:

include_path = "foo/bar"

Then check what phpinfo() says in apache about the include_path.
Note: this works fine for me..

Also, your configure line is kinda odd. Using --disable-all and only 
enabling what you really need would make the line quite more 
readable..

Okay, the issue seems to be resolved - but in the meanwhile I downgraded my whole system to 4.1.2; maybe there was some problem caused by the compiler? I was running gcc-4.3.3 previously.

By the way, my configure line looks odd since it is a gentoo ebuild - it needs to disable virtually everything in order to enable the user to add features by the USE flag.

I think we can close this bug now; but maybe someone can re-test with gcc-4.3.3 again?

Gentoo builds are flaky at best..

Excuse me, what kind of answer is that? The result would have been exactly the same if I had issued the configure line by hand.