I've checked my settings and both handcent and touchdown are still set to vibrate always when receiving an incoming message. The last two days the vibrate has stopped. I usually set the phone to vibrate at work (using beautiful widgets vibrate widget, and audio control widget). The audio control widget has the vibrate box checked on alerts and phone calls. Actually come to think of it, phone calls don't vibrate like they are supposed to either. I just look over and notice the LED blinking to know that I've missed something.
As mentioned I've checked the settings, tried rebooting, did a battery pull. Not sure what else to try.
Not Rooted, 2.1 Droid