Hi,
First off, make sure your iTunes media folder is properly added to Subsonic as a music source. This process is outlined in the Getting Started guide
here.
Remember that Subsonic uses the directory structure to arrange your music. Are you certain that you're looking in the correct folder? Look and see how iTunes is arranging your music... maybe you're just looking in the wrong spot.
Once you're sure the source is correct, try using the Search utility to find the missing music. It couldn't hurt to refresh the search database before you do that. You can refresh your search database in the Settings area for Search.
I highly doubt Subsonic is just choosing to overlook certain folders. I have a fairly large music collection and I've never experienced an issue like this.
Cheers,
Kirk