Hi, I'm lazy but since I wrote a program called filexer to sync uploads I'll just make a couple of nitpicking suggestions.
If you are dealing with remote mounting of windows shares do a lot of testing. In particular permissions and you-can't-get-there-from-here took a lot of my time.
I used a cygwin binary at one point to solve a problem windows wasn't helping me with. It was a while ago and I don't have the code online right now, but I'm pretty sure I used cygwin's touch command.
Granularity < 1 second might flub it.
Illegal characters esp. colons, questionmarks, non-western encodings, filename lengths, etc. if you are actually copying across net like I did. Likewise if so, then security issues possibly.
maybe loading interpreter and scanning program are going to take a while too. Consider running under mod_perl (even if just under cgi emulation) and calling once evvery 10 seconds via a crontab? I don't want to think of any perl program being launched on my system from scratch every 10 seconds.. that is, can you just keep the thing running all the time instead of quitting it after 10 seconds. Much better then I think.