Ed, Ran into this issue. Typically, these are not false positives.
- The files that were supposed to be patched werent-in this case make sure the FSL output is enabled for CSV reporting-it will point you to the exact microsoft KB to download and manually install
- The software is no longer supported by microsoft(example .Net2) thus SCCM won't patch it-in this case uninstall the old unsupported software and install the correct version
- Superseded-this is the worst case scenario as you will have to cross reference the remediation recommendation to determine if it is superseded for This OS-if so, mark as a false pos. If not-it's valid..see one of the two solutions above.
Another, less likely alternative, is that it is due to orphan files on the target system. These are files that were associated with an application/feature on the system that was either removed or upgrade in the past and not all the files were removed properly. Or you have another third party (non-Microsoft) application that requires certain files on the system that are related to Microsoft products. In either cause these issues tend to take time and effort to track down and resolve.
You just need to really examine the FASL Output in the reports and investigate the affected files identified.