Agreeing to everything said.

I also had this Problem. Mine was, that I had a panel.target_map set to an entity bu not reset when loading a level. It is really dumb to not get an error message, but you have to live with it.
In the worst case it is a memory leak and it will haunt you in your dreams..
And you have to rewrite everything from scratch.

What you could also try:
Remove all skycubes and try reloading again