Sorry it's taken so long to get back, some other things came up. After some digging and talking with a rep from DT the issue appears to be related to the following error, like you said, and improper PID tuning for higher velocities. I'll try re-tuning the gains and see if this helps.
As for the synchronization, I'm hoping this stems from poor tracking as well, which may cause one motor to fault while the other continues to run. If I get something to work I'll post back with the results. Thanks!