I've hooked up the encoders and the counts are working on both channels.
I'm not really sure the change from last night. I added back in my servo drives in ethercat-conf.xml so I could move the XY stage around to test some home switches and it was working.
I was working on in the morning trying to get tigervncserver running and did some apt-get update & upgrade. I was doing that last night too when trying to get the updates you were posting. Perhaps I only got the latest update when I did it again this morning.
In anycase, thank you again.