iTunes says one thing, iTunes folder says something else...

Yes, consolidating will fix that.

Did you check the Podcasts folder for stale episodes?
Sometimes you delete stuff and answer "No" to the question if iTunes should delete the files from disk, it happens to the best of us.

I truly don't think consolidate will fix this, but you can try.

It will copy anything outside of the iTunes folder into it (and leave the original copy wherever it was).

You should consolidate to another folder.

This might at least allow the OP a folder to compare to the original.

The consolidation function looks at your iTunes Database and if the song is there, it make sure that that file get's copied to whatever you have set as your iTunes folder.

If you do a consolidate to a folder other than your iTunes folder you could then at least compare the two contents and find out what is in the iTunes folder that is not in the iTunes library itself.

Alternatively what the OP might want to do is go file->add to library and choose the iTunes Music Folder and let it readd everything in it. It should ignore files already in the library, but some duplicates might be produced, but it should certainly bring in anything in the iTunes folder that isn't already in the library.

This is what Apple's help file says about consolidation:

Depending on how you've imported songs, videos, and other items into iTunes, your library can include items that are located in various places on your computer's hard disk or other locations.

You can make sure that copies of all the files in your iTunes library are in your iTunes Music folder so that, for example, it's easier to move your library to a new computer.

To copy all your iTunes files to your iTunes Music folder:

Choose Advanced > Consolidate Library.

Any iTunes file located outside the iTunes Music folder remains in its original location, and a copy of it is placed in your iTunes Music folder.