The default timeout for FCGID is pretty low I think (maybe 5-10 seconds). This was causing me SO much grief that I was just about to lose it. I found these posts out there that helped a lot:
Of course Ubuntu uses different config locations and such for FCGID, but the configuration names are the same.
I set my timeouts to 2 minutes just to be safe. Besides for an admin application, I could wait for a long time without thinking things were amiss. Anyways, help that helps prevent some folks from losing their minds.