I'm not sure I have the same issue, but I had a lot of random tracking aborts with my SW EQ6-R Pro. Jasem researched the problem and it looked like the mount was sending occasionally random position information back to EKOS. So he suggested disabling aborts due to these positional communications by doing the following:
Go to INDI Control Panel --> EQMod --> Horizon
Then uncheck "Abort Tracking" and also set Limit GOTO to "Disable".
Finally, go to INDI Control Panel -->EQMod -->Options --> Configuration --> Save
It worked for me and (best I can determine) doesn't have a downside. EKOS will still abort tracking based on the altitude parameter set in the mount tab.