I have the same problem and have mostly narrowed it down to an interpretation (or misinterpretation in some cases) of the ID3 tags. Things like band names being misspelled in one track out of ten will result in an icon for 9 tracks and a separate icon for the 1 with the spelling error.
However, it seems to go farther than that. Another example is an album I had with the artist name in both the album artist and contributing artist fields on some tracks, and just the contributing artist field on the rest. This also split the files into two groups.
Plus there seems to be a problem with Windows 7 reading the ID3 tags on some of my older rips: it just ignored them completely and separated each song into a complete mess of icons. The only way I could fix that was to re-rip the original CDs with newer software.
I know it's not much help, I'm still working the problem myself, but at least it might give you a place to start.