Hi guys, possibly a bit late to help you, if anyone else has the same problem this might elp. There doesn't seem to be much about this on google.
I had the a similar problem and this fix worked for me.
My problem, after using bytafont, I lost font in my phone dialler, which just crashed when any number was pressed, and i lost font in my keypad, leaving question marks on keys, but it still worked.
The fix is on the bytafont website, in the FAQ page,
My BytaFont is lazy! | BytaFont.
I followed the instructions, but what i did notice that the fonts called PhoneKeyCaps.ttf and PhonepadTwo.ttf were missing from the directory. So to minimize risk, if you notice any fonts are missing, just drop them in and see if that solves the problem.
Good luck.
Edit: this was for iphone 4 running 5.0.1 with bytafont 1.4.1