https://www.youtube.com/watch?v=oCilndqSqKQ&feature=youtu.be

I just wanted to add that after some testing. I came up with the conclusion that it is primarly happening for me while moving upwards with the machine. It also seems to happen in frames that are not touching other project red blocks besides frames. Another thing that disappears quite often are transfer pipes from extra utlities.

Is there a reliable way to reproduce this?

Try something like this:

And crash with Thermal Dynamics, i install 5 redstone energy fluxduct and i get crash on 3 move.
http://pastebin.com/V1YCyeUR