Please file bugs to https://github.com/Brass-Monkery/Multitouch-Bugs/issues. Alternatively, you can email me at email@example.com.
There’s a checkbox in preferences for “Restart on wake” that should help you out. That will only restart the app (not your mac) on wake, so let me know via github or email if that doesn’t fix it and you actually need to reboot your mac. Most Macs don’t have this issue, which is why that checkbox is not enabled by default.