Still waiting for a solution!
I ran out of ideas. I replaced the Hall Sensor with a new one from Beemer Boneyard and my problem - similar to yours bcusack - my problem persists. After three weeks of chasing possible solutions I have run out of tools and skills. I had my RT picked up by my dealer and they will hopefully get to it this week. I'll report back when I get "the call."
R1100RT Runs bad - mine too - similar problem
Stopped at the shop today. They pulled the head on my R1100RT - same symptoms as the OP. No compression on one side; there was a 1/4 inch chip missing from one of the Input valves. I'm glad I did all of the fuel supply maintenance - it was due anyway at 105k miles. And clearly my HES was in poor condition and could have stranded me in wet weather, even though it wasn't the cause of this engine failure.
We'll get together in the next day or so to decide on the scope of the repair work. Might just go for a top end overhaul at this point.