Hi Perrin,
You'll need to do some debugging on your code. The things that are most likely to be different in a persistent environment like mod_perl are environment variables, your current directory, the user you're running as (file permission problems often show up this way), CHECK and INIT blocks, or assumptions in the code about -M filetests. There's a good summary here:
The entire code is written in c :-( only some helper subs are written in perl. I could only write perl ....
regards, jens