Art,
At the risk of driving you to drink, I've discovered some more information about the encoder actions in Darwin that might be of use to you.  As you might recall, I have 3 shaft encoders that work fine in M3.  While playing around in M4, I've found that enabling encoders 0 and 1 results in both axes working fine.  If I disable encoder 0, encoder 1 stops working.  If I enable encoders 0 and 2 only, both work okay.  If I enable all three, I'm back to that problem of Darwin sending signals to M4 when there is encoder motion.
So, enabling encoder 0 seems to be required for any encoder to work.  Encoder 2 seems to interact in other ways.
I bring this up now because it appears that M4 now supports encoders.  Now I need to get the function calls and definitions!
Thanks
Peter