Sorry to necro this topic but I've been having the same issues and seem to have found a respite that doesn't involve losing alot of work.
In 2D mode, between pressing escape to close the message, press T+M and enable everything under Bodystate in between pressing esc to close that error. Delete all the shapes that appeared on on your board, again, in between pressing escape. Recompile, Escape, Save, Escape, and close and reopen. Seems to fix the issue.
It only seems necessary to do to the problem part.
Hope this helps.