Hi,
I have no idea why it worked, but what I did was install the latest update, then (if I remember correctly), do a reset to factory settings, turn the amp of and on again and then let it sit there for at least 10-15 minutes with the app open and connected before I tried saving any tones to it.
This was pure luck, because I had given up and was just playing guitar for roughly 10-15 mins with the app on just one tone before I tried it again and it just worked. Try leaving it even longer.
The other thing worth trying is clicking on the amp icon in the app and seeing if it recognises multiple banks of tones already on the amp. If you don't see lots, then it hasn't finished synching with the app.
Not sure I can add anything else, because it just sort of fixed itself.