When compiling PHP statically with Apache I've observed the following strange and very frustrating behavior. 

in /php
./configure OptionA

in /apache
./configure --activate...
make

then phpinfo() reports the proper ./configure line it was compiled with.

Then do something like
in /php
./configure --without-mysql

in /apache
make (using earlier ./configure)

now phpinfo() reports the old configuration line, but Mysql for example is now not present. 

removing config.cache between compiles in /php doesn't fix things, but a make clean does. Doesn't appear to depend on the /apache build process since make clean on the apache side changes nothing, not does a new /apache ./configure. 

The functionality changes properly in every case. A /php ./configure WITH mysql generates the mysql section in phpinfo(), but the phpinfo() configuration line might remain --without-mysql, even though the mysql extension is listed in the very same phpinfo.

Now I'd call this so much nitpicking if I wasn't going to building php a couple of hundred times. I'd obviously like to avoid doing a make clean between each slightly changed build.

Since the underlying functionality seems to change properly I'm assuming I either missed some obvious instruction, or that there is simple bug or documentation update that should happen to fix things up.