Second trip to dealer for the problem appears to have fixed the problems.
Some notes from that second visit that might help others:
1) It matters which sensor they replace with, guessing some older parts just continue the problem.
2) The shop supervisor had to be involved and talk to BMW tech line and fiddle the adjustments to get it all just so.
3) Perhaps most important the motor that actually closes/locks the top at the windshield fried while they were doing the adjustments and had to be replaced. My gut tells me this might be part of the problem
Everything has worked just fine since then (fingers crossed) and dealer was very generous in charging me really just for parts on this second round, I'd guess they picked up 4-8 hours of tech labor.
2006 650i convertible
2003 525 wagon
1999 M3 sedan