I believe I have a similar problem, if not the same.

I use Facets as my Library Viewer.

Now my music is expanding endlessly, and I want new things to be added rather frequently. This is easily done with the Rescan Media Library function. However, when using this function, Foobar counts 24500 tracks in the library. When adding my music folders manually, Foobar counts 25500 tracks. So for some reason Foobar just ignores 1000 tracks and I can't figure out why. It's extremely annoying because I don't want to have to browse to the file that happens to be missed every time I want to listen to it. What could be causing something like this?

@Vitz: Your problem could be based on missing tags. Try querys like:
%album% MISSING
%artist% MISSING
%title% MISSING

You can query this at once by placing OR between the querys.
That should cover most songs. Make sure you fill the missing tags and the problem should be solved i think.

what if i have the same problem, but all three mentioned tags (album, artist, title) exists in the mp3's id3 tag?

it's a bit weird, as if it doesn't search all folders within a folder. i have U:\anime\ in the media library list, but it doesn't detect anything in U:\anime\tsubasa翼\ (sorry for a chinese figure). i'm 100% sure that it has nothing to do with that chinese character though, because if i include U:\anime\ and U:\anime\tsubasa翼\ then the songs appear.

sorry if this sounds like a stupid question, but i'm quite new to 0.9.x, been using 0.8.3 for years till about an hour ago. this missing song problem is driving me nuts.

When I add new tracks without using Foobar and then do a "Rescan Media Libray", Facets doesn't update the total count of tracks (although the tracks do appear in the list). To make Facets update the count, I just change the selection to something (like say I click on the first genre / album / artist in one of my Facets "view"), and then revert it back to "All". After that, Facets shows the correct number. Hope it makes sense.