When I was fitting people with footbeds I said expect to come back one to two more times for minor tweaks to make sure they were perfect. You may need that. Or as you mentioned your feet might need to get used to them just a bit. What's going on is they're helping to retrain your muscles in your feet which explains why instead of 4 to 5 times you took your boot off it was only twice. Call your fitter, see what they say and just explain the whole situation. The big thing is maintaining a dialog between the two of you.
Thanks for the feedback! With the tweaks you mention can they do this to the current custom footbed, or do I need to remake a new one for eg front foot only?