Open My Computer and goto Tools > Folder Options. In the View tab make sure of the following;
1] "Show hidden files and folders" is selected.
2] "Hide extensions for known files types" is not selected.
3] Temporarily de-select "Hide protected operating system files (Recommended)". After your test, re-select this.
Then, navigate to your audio file folders and look again. You may find hidden files, (perfectly normal).
Also, in the My Computer display window, click the column header for "Type". This will list your files in file type order. That may help you track down non-audio files.
I've added my collection to iTunes and Winamp, both are reporting 22,978 files, however windows reports 23,000 files. I deleted all jpg's and other assorted files in the mix. I even used a command line to search for files that didn't contain "mp3", and nothing showed up. So my question is, how can I find the culprits? Thanks a lot