There are numerous posts here with the same question. It appears that calculating registry health is an imprecise science. I posted a similar question recently, asking why my registry health is at 98% when I scanned my WinXP SP2 machine with Registry Cleaner's most aggressive setting and fixed every error it found - I thought the result should have been 100% registry health. No one could really answer the question, so I went away happy that my machine is running better than it ever has.
Did you 'Run quick system analysis...' on the File menu after your scan? This cleans out the program's cache and resets the health indicators.
