Go to settings>sound&display and put a check in box next to Pulse Notification light.
I'm using Cyanogen 184.108.40.206. I wasn't getting LED notifications either and checked this even though the MotoDroid obviously doesn't have a track ball! Any who, this seemed to solve the problem because my LED notifications are fine now.
Very nice, was just about to join the party, but then i read the above post. mine was already check, but i uncheck and rechecked it and now it works. i also checked the other pulse setting just incase, but either way, that is a confirmed fix.
i had the same problem and couldn't get mine to work again. i went back to stock then re-rooted and i'm good to go. might have been the long way but it worked.
I'd rather have a bottle in front of me than a frontal lobotomy.