Check rp_serve_concrete_file in /packages/acs-tcl/tcl/request-processor-procs.tcl. If it doesn't recognize the file it just returns it back to the browser, which skips AOLserver's processing of it. OACS isn't designed to support integration of this sort but it shouldn't be too hard to make it do so.
You probably need to explicitly check for your PHP extensions in the procedure and then return filter_ok rather than return the file in this case. I believe that if you do this then AOLserver will ship the file off to the PHP module but have not tested it myself (nor will I be doing so).
I also may be misreading the source and this may not be the problem at all but it does explain the experiences related by folks above.
