I think now that changing to UTF-16 was just a coincidence - my work around at the moment is to open catalyst and let the Exact mapping load in. Then remove the mix mapping prefs file from the folder and save all prefs in catalyst.
However it's really hit and miss, I may have to go through this process (replacing the newly created mix mapping prefs with the original that has all the exact mapping info). However, when it finally saves i know it'll be fine from then on until I try close down and try open it all again.
I know there's been a couple of responses saying their having the same problem - I would guess it's really straight forward for anyone running sierra to see the problem unless I've got some odd conflict going on.
Also, yes, This was all done again this morning running 10.12.3