I’ve been away on vacation for a couple of weeks, but after getting back I’ve been looking further into that non-collision bug. After some further investigation, it turned out that not only was my “on collision stay” callback not being called, but collisions between the parts were not happening altogether. I also managed to reproduce the issue in the editor as well as standalone / web-player builds.
I haven’t found a work around yet (not sure if I even can), but I put together a special cut down version of my game project and sent it off to Unity to help them reproduce the bug. In the meantime, the game is still broken unfortunately, the only way to get around the issue is by removing and re-adding parts to your construction until Unity physics corrects itself. I hope the Unity devs can fix this issue soon, but I guess we’ll just have to wait and see!