I have been down this road myself... and I believe this is the issue. There is a default directory that php looks for when compiling itself for MySQL. While all the documentation leads us to do the obvious (which is to point the configure script to the appropriate directory), this does not seem to be how it ACTUALLY works.
Just use...
--with-mysql=/usr
That is what eventually worked with me, although I found out I was doing something else wrong, or at least I think I was which was causing an error. I had made a custom file with all my compile options on it with (./configure \ ) at the top and was executing that file, for some reason that didn't work the same as just copying and pasting this info to the console. Who knows what the real prob was.