Have had the same exact situation happen multiple times, if you were trying to deodex and ran into errors with system mounting and or copying the files over that would be why, another reason is the dalvik was wiped. The only current solution I found was to either download aroma file manager and put phone in cwm and use either aroma to copy the deodexed files to their correct location and make sure to use adb to mount the system first, as stated in shinru's tutorial. If that fails, nand backup, or in my case which happened twice I have to fastboot back to stock recovery and start all over. Good luck.