Since you refer to "tasks", I assume you're using the Pro version? I use Home, but I can make some guesses based on experience with that.
I typically get the "Skipped because of settings" notice as a popup over the main summary report -- in my case, it's because I've excluded a set of folders I know are just JPG's, quite a few of them. In standard scanning they (the files, that is) would be skipped anyway because they're not executables or quasi-executables, but I use thorough scanning and the exclusion cuts down the scan time quite a bit.
It's also possible you're looking at the report itself and using standard scan, and you've got your report options set (for whatever reason, or even accidentally) to include skipped files. Take a look at your report options and see if there's anything there you feel you can safely live without and un-tick those.
Best,
Mike