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Sounds like that is pretty much like limiting PHP to a time limit of 40 seconds. Now in php you can use ini_set line in a script to raise that timeout but it appears from what your saying this freeBSD thing does not allow altering settings it needs to be install with specific settings. I have not heard too much about that program but if thats what you must do then by all means do it.
Really you probally want to ask the mod_fcgi people as this is more of a server software question
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