I have the exact same problem.
I use Honeycomb Alpha and Bravo controls. All been working fine for the past 4 months and now these same 'increment errors' as stated here - in 1000ft and 10 degree increments, rather than 100ft and 1 degree increments. So annoying!
I note on my Bravo Throttle Quadrant that buttons 25 & 28 are on all the time, yet I have NO MAPPING of these 'invisible' pushbuttons anywhere. I get the feeling they are assigned for reverse thrust, if I had the four levers plugged in. But as I say, it's all been working perfectly fine until the last week :-(