The System Internals scan detects "Run" entries as invalid if they are not a full path, even if they are in the system environment path.

Example:

Registry Path: HKLM - SOFTWARE - Microsoft - Windows - Run
Key Name: NvCplDaemon
Data: RUNDLL32.EXE C:\WINDOWS\system32\NvCpl.dll,NvStartup

The above entry is detected as invalid.

While the entry for "RUNDLL32.EXE" does not include its whole path, it is in the system environment path (in this case, c:\Windows\System32), so it is not actually invalid.

Any entry that does not include its full path seems to be detected. Spybot ought to check if the program exists anywhere in the system environment path before deeming it invalid. I have several programs that add their own program directory to the path variable.