This situation may be fixed in RC2 ...
This Backup Tool screenshot illustrates several cases:
Notes:
* Fod.dne=File or directory "path" does not exist
* 16 items when restored can create 25 valid items because certain HKCU and HKUS items are sort of "synonyms." That is, restoring one gives you both. There were 8 of these in these cases + 9 other items (8+8+9=25) :)
Impact? Restore does not always recreate the original registry state.