I have been thinking of all the things it might be, (and I'm not on the support team, so my ideas are really just guesses, of varying quality!) Depending on WHAT is in your unit, ie, old files, with old file structures, you could have errors in some old data bases. The idea of backup ALL the files, in your unit, and then just put back what you need, will possibly help. Sounds like you are headed that way already. But, I do know that alot has changed in the LS, in the last year.
It is a product in development... which in my opinion is good.... because it means progress.
But, it has hazards too, such as this issue you have raised.
Worst case, maybe you would have to completely clean out your unit, and put back the coords, as design coords, and continue your job. However, get better advice than mine, before doing that.
N