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The encoder data issue may be electrical noise related.

I guess it could be a Mesa modbus bug but its a bit strange
that it seems to affect physically nearby signals.

How is the RS-485 interface connected to the 7I80?

Also on baud rate issue, the eletec I/O module will not run at 115200
baud reliably, it crashes and can only be recovered by a power cycle
of the I/O module. I suspect a stack error at 115200 baud  interrupt
rates in the I/O module. Running at 115200 baud the card crashes in
a few hours, at 9600 baud its been running a week so far.

use an internet search engine such as Google Chrome Type:
linuxcnc : m6 remap for atc
you get few answers to your questions.