This may not help anyone, but here's what I came up with for now.
I keep two running backups - my 4.3 workhorse, and my 4.4 playground. There are some issues with the 4.4 I think many of us are dealing with - the one that is bugging me the most is not able to move files using any file manager and TIBU not backing up to it.
i think there is an edit to fix this, but I'm waiting for it to be confirmed and integrated, as opposed to doing it each time I update to the newest build.
I have a great deal of my 32 gigs I'm not using on the phone, so I set up TIBU to back up to a new directory ON THE PHONE. This directory is not touched with wipes or ROM changes, so no issues. I can then back up, restore apps when I ROM, and I create ZIPS to flash I store there too. Anything that needs to write/read to sdcard, now goes on my phone. I can still READ from sdcard, so I've not moved ring tones for example.
This is a small issue, I know - but as you nerds get the bits and parts working, I still want to backup - so I don't have to bug you all! This is a short term work around for me.
[ btw - reminder - NERDS, as I've said before, is a term of endearment! ]
Carry on.
Skate