setting the lines

[java]
extension_dir=/usr/local/lib
extension=libphp_java.so
java.class.path=/usr/local/lib/php_java.jar

in php.ini do not affect master values, only local values. 
changing other values in php.ini (e.g. highlight.bg) works fine, i.e. affects both master and local

php runs as apache module, with 
./configure --with-apxs=/usr/local/apache/bin/apxs --with-mysql --enable-track-vars --with-java=/usr/local/jdk1.2.2 --with-config-file-path=/usr/local/lib

jdk used is blackdown jdk1.2.2 (jdk-1.2.2-rc4-linux-i386-glibc-2.1.2.tar)

compile and make run without errors, php works fine, but java doesn't (seperate bug report)