It seems that the registry cleaner is getting confused with the %ProgramFiles% variable and flagging any files using this scheme as missing.
For instance in Vista, registry cleaner thinks the file MSAScui.exe located at "%ProgramFiles%\Windows Defender\MSASCui.exe" is missing, but that's not the case. It's in that location on the disk. It's listed correctly in the registry, but when I removed it, Defender didn't launch properly.
There are a few others too, where registry cleaner is saying that any files where their location starts with %ProgramFiles% are missing, but they are all there on the disk.
Manually editing the registry and changing the location from %ProgramFiles% to C:\Program Files eliminates the problem, and registry cleaner sees them fine and doesn't return a "missing" error.
Any thoughts?