I'm using the directory watcher gateway to log changed files as they are pushed (FTP'd) to a development server. The gateway occassionally misses random files. I've seen some older post where this was a problem and was looking to see if the problem still exists on CF9. The onAdd/onUpdate methods simply write the file details to a SQL database. There is very little logic in the .cfc.
If you FTP 10 files to the server it will tell you 8 changed. If you push the same 10 again it will in some cases it will reconcile the missing files. I have the intervalconfigured for 60 seconds.
My problem was not "randomly skipping of files". In the ColdFusion administrator under Event Gateways/Settings a parameter for "Maximum number of events to queue" is configured to 10 by default. If you FTP more than 10 files in a timeframe under your configured run interval you will lose events. My directory watcher was running every 60 seconds and it was common to FTP > 10 files in 60 seconds. My solution was to increase the "Maximum number of events to queue" and decrease my run interval from 60 to 15. The combination of these two configuration changes has fixed my missing files problem.