Since you said "reasonably sure that it isn't something obvious", I'll just make sure you're "absolutely sure". Have you checked the error log? Must laugh heartily if the problem is logged in there :). Other than that, the only reason I know of would be a call to CORE::exit(). Anything else would have to be a bug, something very screwy, or something very obvious.

update: Is this a pure mod_perl handler or are you using ModPerl::Registry? (For one, the CORE::exit() would only be under ModPerl::Registry, as that module overloads exit() so that any calls to a plain exit() do not actually exit the perl interpreter process)