Some ideas off the top of my head, prolly not worth too much...
Is the script in mod_perl? I don't know mod_perl but from what I understand there is caching involved.
Is there a high load on the machine, or a really high http timeout setting? Perhaps it actually took an hour for those two instances to complete.
Are you sure there's only one copy? The users don't have bookmarks pointing to the old one or anything?