I know there have been some posts about using Maschine causing Cubase to crash when looping, but my issue is different.
If I set Maschine up as a plugin and tricker scene changes by MIDI Programme changes in Cubase there is an issue when looping.
Once Cubase loops back to the beginning it wont re-start the scene at the start where it should do it. It will instead start playing back the Maschine scene a few bars in. Consequently throwing everything out of synch. I have a MIDI programme change right at the start of the loop that should reset the scene, and Maschine is set up to retrigger, with Synch mode off.
This is only a problem when looping.
I am using Cubase 8.5 with Maschine 2. I also had this same problem with Cubase 6 and Maschine 1.