Long-time lurker - first time posting.
I've got my Droid X on the rooted Gingerbread. I used Lightflow and liked it - but I like having different colored LED notifications for specific people via Handcent.
I literally got it working about 15 minutes ago.
Not only did I go into the normal settings and disable notifications, I launched the stock messaging app and turned them off there. The only issue now is that Handcent's "Test Notification" does not work to verify LED function. It takes a real message to trigger the LED. LED Flash Frequency is set to "Normal" and not "Default". Not sure what the difference is, but it's finally working. Play around while having a conversation with someone and see if you can get it to work.
LightFlow is nice, but it's frozen by Titanium Backup until I can get it to play nicely with Handcent. Hopefully I can selectively add back functions until I get a working combination.
I had the same problem with the notification light. I tried everything and it finally worked when i disabled "trackball" light. set it to never and the regular notification light should resume function.