I noticed the other day I was having some tuning problems too. So I started reading this thread, it also seemed to have occurred after I had creating a couple of extra custom presets with their own tuning.
I had a bit of a play around in workbench tonight and noticed my drop D tuning had dropped to the high e string. A bit strange so I fixed the patch and uploaded, but I was still having problems. looking around I clicked on the parallel pitch something I'd played with at the same time trying out 6 string versions of the twelve string models and I noticed something unusual. Even though the Parallel pitch was switched off all my models seemed to pitch settings, clearing this then uploading solved the problem. So I then created an "empty" pitch preset and cleared every 6 string guitar. Problem solved, tuning works great again.
I suspect like me most people don't look at the parallel pitch tab much for the non 12 strings, especially with it being disabled. So maybe worth checking just in case it wasn't a one off.