I think I have a fix!
I was hoping the latest OTA that has been hitting our Bionics today would fix the touchscreen "flake out" experienced when the phone is connected to the standard dock and charging with the charger that came w/the standard dock.
Sadly it didn't... it almost seemed worse really. My wife was texting me after my phone updated and I was getting very tired of wrestling w/my phone rather than being able to respond.
On a whim I disconnected the charging cable - phone was able to respond accurately. Reconnect the charger that came with it, it reverted back to making it difficult to type. Finally I swapped the charger out - to the Motorola charger style with the removable USB cable and plugged that into my phone. Bingo! Was able to type accurately AND charge the darn phone.
So, if you're running into problems with the screen not tracking you accurately, try a different charger style. I suspect there is something to do with how the charger, dock, and phone are interacting.
Lastly, Booooo Moto.. bad Moto. I really liked how my old OG Droid dock could be connected to my computer's USB cable and served as a simple USB pass-through when I wanted it. Booooo again for giving us a junky charger that causes the combo do to this.
Hope this helps.