Have you tried dprofpp's -F switch?

One thing that produces a garbled tmon.out file is code that uses the magic goto:

sub bsub {
    return ...;
}
sub asub{
    goto &bsub;
}
[download]

A bsub never returns to asub, no exit timestamp appears in the trace for that sub. -F will fake those timestamps and allow dprofpp to process the file. The fake timestamps will usually be the same as the exit timestamp for the gone to sub</c>, so the timings will all be fairly accurate.

I've never used mod_perl or Safe, so this may be a completely bogus post and waste of your time and mine.