Updated PHP breaks processing-intense Procedure

Hey - -- I have a huge screen -- to make it simple for the user, it does 100s of calls to MySQL and has 1,000s (literally) of POST variables. We have done extensive research and see that upgrading from php 5.1.6-27 to 5.1.6-39 is the thing that caused it to break. All other issues (Apache, PHP and MySQL configuration and Versions) have been methodically ruled out. Anybody experience this? Heard of it? Suggest a repair (other than changing my screen)? *** Please don't tell me to redesign the screen -- this may come, but now is an urgent situation.*** Worked fine in prior versions for the last 3 years. Thanks, Ken