At what point are you going to say this is a bad unit and give the man a new one? Is there a rash of mfm's going bad due to firmware? I have one. Works fine. From a support perspective, this looks to be bad hardware. My two cents. It works, then it doesn't. Then it does for a bit, then stops. No change to anything on the system. Now he's at a halt. In addition, shinook is an absolute duet fanboi. He got ME into the mfm even though I didn't want to. So glad he did because I love it. Let's move this guy forward.
Thans, looks like you are getting quite a lot framing errors (but interestingly, no parity errors). So I think it's likely that the errors are caused by reception of bad data that isn't detected as such. I was already planning to change the firmware to ignore isolated data points that are out of line with other data. I'll bring this work forward, I may vebe start on it tomorrow.
Please post your config.g file, it may help me to reproduce the problem.
Does the filament monitor cable run close to the extruder motor cable (or any other stepper motor cable) for an appreciable distance?