Hi TheBiles,
This warning is really important - it means Titanium Backup could *not* acquire the root priviledges - so you really *need* to solve this problem before doing any backups or restores. Otherwise your new backups will be broken !
I believe that some root apps might work properly, but that problem might happen with any new apps that you install. Try for example to add a terminal app like "ConnectBox" or "Better Terminal Emulator". Then type "su" and then "whoami" inside that app. Just like Titanium Backup, you will not get "uid 0" in these apps. This really means there *is* a problem either with your "su" executable or with your "Superuser Whitelist" system app !
So far, about 10 users have had this "no uid 0" problem, and *all* of them reported to me that they did solve the problem by fixing "su" (and/or the "Superuser whitelist" system app).
Please look if there's any fix that you can apply regarding this. Also check that your "su" and "Superuser whitelist" are really compatible with each other. Then your problem will certainly be solved.
Once the problem is solved, if you have the Donate version you are strongly advised to run the batch verifier.
Thanks - and please let us know how it goes !