I can't diagnose what is wrong, but my first question would be, How did you do your clone? If you did it with Penguinbait's Console Tools deb, you could try running Console Tools' options that re-do the boot menu.

Otherwise, I'd do the cloning again, but I'd start with Penguinbait's deb. You can make a backup of your internal flash with the standard NIT back-up utility first, so that re-creating your programs and docs, etc., will be easy.