This is a last resort, but I can not think of anything else to suggest.
- do a factory reset
You will probably lose your jailbreak, but that does not matter.
- follow Amazon's directions to update your Kindle, see:
http://www.amazon.com/gp/help/custom...deId=200790650
- use the regular, 5-series jailbreak (it will work on the most recent KT firmware).
- install KUAL
- install MrPI
It is not required, but makes installing other things much easier.
Then check again for the 'disappearing' files before doing or installing anything else.
I have a B00F model sitting here, with exactly the above done to it, so I know that yours **should** work when your done with the above list.
If it does not, let us know (again).