It's been fixed :D I had contact with RYK and they were very responsive and helpful. They instructed me to do some continuity checks the trace they've send me lead to IC9 (on the bottom left IC on the main PCB). This IC is responsible for the midi input I guess and it had a leg that was not soldered properly. Added some extra tin and the module works like a charm. Updating it through sysex was a piece of cake as well.
The module now works as intended for me, as the newer firmware has the option to use the midi input as a clock reset. This method is solid and patching the reset from something like a euclidean rythm is really fun.
Props again to RYK, their support is very responsive and even though a third party build it they were willing to help me sort out the problem.