I lean to the same explanation as Andi B. But before you install a new kernel, you need to access the disk again. After booting from the reserve partition (or in your case better from the installation cd) to get a newer kernel running during your restore session, and issue the command "chkdsk /f c:". This ought to correct your disk problem, at least to the stage that you can reboot in the ordinary way and see if the problem reappears. If it does not, you are probably fine, continuing with the old kernel, but I would still advice you to move to a newer kernel as changes to eCS presumes 14.104a_xxx or newer.
I run bootable JFS (but with the most recent kernel: 14.105a_SMP) which works beautifully with bootable JFS).
Good luck! Eirik