Does the copy of Heroes 2 Gold Edition sold on gog contain the "alternative" sorceress theme?
I don't know why I can't have links in my posts, but to know what I mean, go to youtube and search for these terms: "shyranis heroes 2 gold sorceress alternative" and click the first video.

Also, what format is the music in? Is it still CD quality like on the original CD (since gog uses digital downloads)?

No. Assuming you mean Heroes II Gold from HoMM Millenium Edition. It's in CD quality but I'm pretty sure this CD image is homemade (therefore, quality of the audio tracks is questionable).

Is anyone having problems with this soundtrack? Half of my tracks are fine, the other half can't be played by WMP and show no associated track data.

I read in some forum that the track you mentioned was actually from HoMM III. So confused, what is it doing there??

What, they still haven't fixed that? I pointed that out to them years ago!