I'm thinking you must have not had all the required files for the phone to load correctly in your framework-res.apk file.
If the phone cannot find the pictures or other files needed, depending on how dependant the system is on it, it may not boot up completely, or force close when it tries to open a non-existing file...
You don't need to do a nandroid backup for it to get better, just flash a working theme on top of it while in recovery and it should work again just fine!
As far as
why you had an incomplete framework-res.apk file, there may be many reasons...
Are you using linux? If so, are you using the command line to rezip your framework-res.apk?
if so, it might just be that you've omitted the "r" in
Code:
zip -0r framework-res.apk file1 file2 file3 folder1/ folder2/
without the "r", it won't store recursively, and folder1 and folder2 would end up empty... In other words, your framework-res.apk/res/ folder would be empty in your particular case. Is that maybe what happened?
EDIT: Actually, on re-reading your post, it appears you did it all through android. So maybe the app you're using has an issue, or it was a weird bug. If it happens consistently, I'd foresee an email to the app developper to let him know of the issue in your near future...