Will test it out straight away, good job!
I and everyone in my team are very impressed by your swift action in regards to our issues with step pulses. I hope we can figure it out together, both for us and, of course, the community.
Would it make any difference if you had remote access to Atmel ICE kit connected to our devices? If so just send me an email!
Also, do you think it would help us anything if I hook it up and does some trial-and-error to see if I can get more verbose logs or something like that?