Perhaps you know, that USB with TMCM uses a software driver emulating RS232.
Perhaps that emulating driver has some bug.
The driver might need extra configuration. Did you try it?
In general, the main problem in such situations is a rate of flow of data - either too fast, or too slow, or intermittent. This needs investigation. Seems like a bug in TMCL-IDE.
You did try to send command GAP continuously as a test.
There might be still a difference between GAP and Stall Guard profiler.
In case of GAP command, a microprocessor of TMCM does not have anything much to do. It simply returns. I don't remember though. Maybe actual position parameter still needs to be retrieved from TMC428.
In case of a Stall-Guard profiler, the processor has extra things to do, like retrieving the status of load from TMC428.
That's where the minute fluctuations of time might affect the result. Consider that USB is sometimes faster than RS232. So the period of data exchange is shorter, perhaps the timeout too.
Inside TMCM the motion processor TMC428 updates the Stall Guard value (the load) from driver TMC246 only each full step. So, some durations of steps might simply be longer than the timeout in USB.
Also it is possible that the USB connection is simply not reliable at some rates. Did you try to vary the baud rates?
The other possible fault might be in the USB circtuitry of TMCM610. Maybe it introduces some voltage to TMCM, where it should not, so that it interferes with Stall-Guard specifically. Maybe it interferes on the SPI line between the TMC428 and TMC246 on board of TMCM610.
This is for Trinamic to investigate.
But one indicator is that most problably the connection to module is not lost at all, and the module itself remain perfectly operational. It might even retain the correct count of steps made so far till the fault.
All that happens is that communication fails but temporarily. Does TMCL-IDE continue to operate? If it does not, did you try to restart TMCL-IDE without restarting the TMCM? Does TMCM610 remain operational?
Did you try to install a new Firmware 6.22 for TMCM610 ? Did it improve the problem?