The "jail break" is a single file that is only ever used or even touched when checking the signature of one of our packages.
Only that 256 byte file, the actual signature handling is still Amazons.
So it is impossible for the troubles you report to be due to the jail break file that is present.
And keep in mind, that if the Kindle ever has a chance to call home, it will update to the current firmware - - which you will find is impossible to jail break.
That is: you are setting yourself up for a one way trip.
So I hope you enjoy your stock Kindle, the one that still will not show you your books.