I looked through the older posts and did not really see this specifically.

I have two kinects (at 90 degrees), newest version demo of everything.

Very carefully followed all the calibration steps, measured everything.

I am frequently having a problem with arms doing weird things, folding into the body, or just otherwise not being anywhere close to the correct position. You see the correct position clear from the background, but refit pose does not seem to lock on to it. manually moving the arm there does not fix the problem either, it quickly strays off again.

Sadly this was done with a model, so I cannot just re do it.

Tracking algorythm may lose arms when they are too close to the body - depth difference is very low. If this happens with arms distant from the body - most probably the calibration is not good, and camera positions are incorrect. Make a screenshot of some "lost" frame with "Skin" unchecked and "Show depth from all sensors" checked.