This may not seem related at first, but hang in there.
I used to have an OG Droid. At some point I purchased some off-brand wall chargers. When I would use them, my phone would start freaking out, typing random things etc. It was as though an invisible finger was messing with the touchscreen. The phone was still fine when I use the OEM chargers. I could use the off-brand ones as long as I locked the screen. Anyway, I don't know much about electricity - but it is my understanding that these are capacitive touch-screen which means they are affected by electricity. If something electrical was just a little off in the wall charger I guess it causes the touchscreen to react as though it is being touched.
The off-brand wall chargers do the same thing with my new Bionic. I understand you are using the Motorola brand dock - but maybe there is something off electrically in either your dock, the wall plug, or your phone? I realize this is *way* late but thought it might be helpful to others.
I got this issue resolved.. Turns out it wasn't the phone or the charger; it was an app I had installed (Seal). After factory resetting, I started loading my apps on there one by one until I found the culprit. Uninstalled it and got another app locker (App Locker Pro) and now it works like a charm :biggrin: