I have had this problem and fixed it multiple times...
The problem is, that for some reason the stock file editor sometimes does not save the full file, then starts crashing, etc. Other file editors seem to work ok.
By the way this can also happen for some reasonwhen applying icon packs or themes.
Now the good part - you can fix it without even loosing you data. You need to flash only the system partition from the stock image. Follow this:
But in step 3 apply the command: fastboot flash system system.img
Skip the rest of the steps and apply: fastboot reboot.
You can get adb and the Android SDK tools to use here: