Finding the common factor in the incremental advancing is somewhat critical, as it may be related to the similar issues lil-bent had with his LS installation, and perhaps others. It was difficult to get clear info in that thread, so maybe we can sort it here.
Incrementally advancing ignition strikes me as being a tooth count issue. ie The classic case being when someone enters a 36-1 wheel as having 35 primary teeth (Because that's how many there actually are on the wheel). It results in the crank angle tracking becoming out by a certain number of degrees every revolution.
lil_bents problem was different I think, definitely some misconfigured decoder stuff happening there in combination with some noise.