I have the same kind of problem but mine is that the unit show 96kHz while the project change to 44.1 automatically; and I cannot set it back to 96 unless restart Logic Pro X.
I found that I can open the former project, which I fortunately can work at 96kHz, and duplicate the project to save as a new project. It works properly as it should. Anyway, I still wait for a real solution from Steinberg.