I've got the same problem migrating some clients apps to apache 2.
The script which under apache 1.3.x runs in 2 minutes, times out after 12 on the new machine. The new machine is about 4x faster than the old. I believe in my case, it's a bug with apache and it's new filter system. I made it a command line utility and it runs in about a minute. So I've isolated everything else (the filesystem,db, process size)
It doesn't fork anything BTW.
I've read various things that indicate under certain circumstances, that Apache 2 reports prematurarly, the wrong content length because of the way it chunks output for the filters.
So first, try speeding it up or increasing the timeout parameter in Apache. Second, Pray. Every report of this I saw while researching, none had an answer (Google with the timeout error text ). (Redhat hasn't been able to come up with anything for me.)
If I find anything out, I'll be sure to post an answer and would appreciate it, if you could do the same.
-Lee
"To be civilized is to deny one's nature."