I’ve got Mychron 3 plus, the one with the box. I’ve also had a standard Mychron with out the box on a Rotax. I have my rpm wire wrapped around the plug wire 3 or 4 times and then zip tied. Never had a problem reading RPM unless the settings on the Mychron accidentally got changed.
Try wrapping you RPM wire around the plug wire first and see if that solves the Mychron problem. If if doesn’t then I’d trade Mychrons with someone. If that doesn’t work then it would more than likely be the Rotax.
I had a weird electrical issue with my Rotax. Sometimes it would start and then others nothing. It would sometimes die taking off on the grid. Ended up being the ground wire on the coil relocation bracket. I recently removed it and had the ground wire on the opposite side of the coil bracket changed it to the other side and worked perfect.
Also check the crank sensor plug on the bottom of the backside of the motor. I had one that came loose and it would cut out badly at higher RPM’s.