Just to update in case anyone else has/d same problems as me.
I tried different things, updated to newest nightly (19. april), I still had same issues after that. Reformatted cards. I deactivated raw_twk module and these broken frames became more rare, but not completely gone.
So I reverted back to a build from February 20th. I believe this is the last build I was using before updating to the merged FRSP build (29. Mar) and I started getting broken frames.
Recorded a lot of long shots with low light, high light, changing light and what not, just different stuff to challenge the sensor, in case that was causing these broken frames to be written to the card and I did not have one dropped frame or broken frame.
I am sorry that I can't give a more technical idea to why I was experiencing these issues. raw_twk was causing the camera to crash everytime I took a picture with FRSP, so the raw_twk module had to be deactivated and the module might have had some kind of interference with mlv_rec too, I don't know.. It seemed like the broken frames were much less occuring after I deactivated the module. Before I did that I experienced broken frames in almost every shot and often several times.