This problem seems to take many forms, as evidenced by the bug database, but from all the entries I have read, none seems quite like what I'm seeing.

I've been using 4.3 from CVS since about last June, and set up my php.ini around then, and I have not really touched it since (not the problem). I've stayed with CVS versions ever since, until today. I started having a compilation problem with the cvs version (Separate problem), but I still needed to rebuild PHP so I grabbed the release 4.3.0. This compiled (using the same configure I've been using all along) with no problems so I installed it and got file not found errors all over. phpinfo reveals that everything is at defaults (include_path at default value was causing my errors), i.e. php.ini is being ignored. I recompiled several times specifying many different locations for php.ini, but none worked.

So now it looks like maybe a permissions problem, Except that the php.ini is the same file that has been working for many months with cvs versions up until yesterday - this is the first time I've tried using a release version. Whatever, all permissions look fine - the www user has no trouble reading the file.

I thought perhaps the format or content of the ini file had changed, so I built a new one with my settings in from php.ini-recommended. Made no difference, but was probably a good idea anyway.

Eventually I found the bug report about php preferring /php.ini over the compiled in location, so I copied my old php.ini there and it did indeed pick it up (a temporary workaround), So now I know there's nothing wrong with what's in either my old or new php.ini files (I don't seem to be seeing the current open bug about php.ini based on recommended not working).

So the only remaining variable is that I'm using 4.3.0 release, and not a CVS version. Everything else is identical. I can only surmise that it must be a release version bug. I would like to confirm this by compiling a CVS version and have it work, but as I mentioned, it's not compiling for me right now, so I can't test that.

Just for good measure, here's my configure:
./configure --with-apxs=/usr/sbin/apxs --with-mysql=/usr/local --enable-exif --with-gd --with-jpeg-dir=/usr/local/bin --with-bz2 --with-zlib --with-openssl --with-gettext --with-ldap --with-mhash --disable-overload --enable-sockets --with-mcrypt --enable-sysvshm --enable-pcntl --with-config-file-path=/var/www/conf --enable-mbstring --with-pear=/usr/local/lib/php --enable-bcmath --enable-gd-native-ttf --enable-gd-imgstrttf --with-freetype-dir=/usr/local

Extracts from phpinfo:
With /php.ini:
Configuration File (php.ini) Path /php.ini

Without /php.ini, (ini in specified place)
Configuration File (php.ini) Path /var/www/conf/