It sounds like you have all your songs in the correct directory structure on the hard drive, so I don't think that is an issue at all.
How are the individual songs names in the artists/albums folder, are they named like:
Are your songs all correctly tagged with the artist and title of the song? You mention on some songs just the title is showing up. This sounds like you are missing the tag's in the MP3 files.
Artist Name - Song title.mp3
Open the Road Runner Config utility, and click on the music tab. Under "Use Id3 Tags" try setting that to not use tags. If you songs files are named correctly, and in the directory structure you mentioned, this should work.
It really just sounds like you need to get all your MP3 tags in order, to make everything show up the way you want. It is a royal pain, and time consuming, but is something most of us have been through before.