FWIW, I have never had any problems like this using SuperDuper! In fact, I use SuperDuper! because unlike Disk Utility's restore option or Carbon Copy Cloner, it does not use
asr, which does block copies when possible. (See the "HOW TO GET THE FASTEST RESTORES" section of the asr link for more about this.)
Block copies are faster that file copies, but will preserve directory errors if they exist & do not perform any defragmentation or directory optimization, since they do block by block copies without going into the file system. File copies are slower, but because they go thorough the file system, they halt with an error if there are directory errors, & when used for cloning will automatically perform file & disk defragmentation because the files are written sequentially. (This is not true for incremental updates like SuperDuper!'s "Smart Update" feature.)
For this reason, if you use SuperDuper! you are unlikely to get any benefit by using Disk Warrior on a freshly made clone. The same would probably be true if you used a cloning utility that used asr to do file copies, but it could be beneficial if they did block copies.
Assuming the renaming issue is related to Disk Warrior, as suggested by The hatter, this may help you avoid it if you continue to use SuperDuper!. Of course, whatever you use, make sure you have the latest version(s) & that they are fully compatible with Snow Leopard.