Automatically run a script on an uploaded FTP file
You don't state your OS, but if you're on a Linux box, you can hook 'inotify', which will is a kernel subsystem that fires when filesystem events happen. This should give you much better response time than cron, which only runs on one minute granularity.
The following link will get you started, but there are Perl, Python, and a bunch of other bindings available.
http://inotify-tools.sourceforge.net
If changing your ftp daemon is not a problem then pure-ftpd has this functionnality.
Hope this helps.