I have a similar problem. Windows Media Player recognises any downloaded tracks as "music', but all my CDs that I have copied onto my computer hard drive as 'other media', which don't appear in the list picked up by Windows Media Connect. ('Groundgripper', try clicking on the 'other media' tab and you might find your missing music files.)
I believe the problem lies in the fact that the CD music is missing an identifier that can be added to each track, but in the short time I have at home between trips, I have yet to discover how to go about this.
If anyone could show me the way, I'd appreciate it.