First, GOG's installer registers the game with Game Explorer using a GUID of their choosing (like any modern game labelled with "Games For Windows" does). The way to register in 7 works just as well in Vista (and has always been the official way, only Vista was more relaxed in what it accepted [not fully finalised, I believe] so GOG and others did it in a lazier way which is no longer accepted and produces the unusable icons under "Unspecified")
Second, Windows Vista's or 7's built-in "Legacy Games Detection" finds the game and sees that it is not registered in GE - because the GUID it expects is not present - so it registers the game with the GUID it does expect. Because it is a legacy game - created before there ever was a game explorer, much less have he installer use hooks for it - it surely can't be registered, right?
There may be more to it that just GUID matching, so something may get severely messed up if GOG just changed the GUIDs they use to whatever Windows expects for each game. I assume there is a pretty good reason they have not done so.
both windows vista and 7 have a legacy game scanner if it sees an exe with a certain checksum it loads a simple profile for it. gog.com loads a different profile with the shelf art and there contact info the one windows makes has the allgames.com info. gog.com should talk with Microsoft about getting proper guid codes done for the titles or only do ones for games who do not have ones to begin with like the Dos titles that all have the same checksum.