I assume that's because they know that everybody wants the classic Goldberg theme, but there's either some licensing issues or something that means that they want to use their own WWE theme for him.
So, give him the classic music for the big return, but then he gets the WWE version from there on out.
Would doubt its copyright issues, wwe just seem to like changing themes for their own versions wherever possible. Even Sting had his wcw theme in the promo' vids yet for whatever reason it was a wwe theme when he actually wrestled. Even Bret Hart off-air when he appears in wwe has his 1997 theme, yet for tv segments they use that "return" remix. Vince apparently hates to pay for music to use as he has an in-house composer, wouldn't surprise me if it was the fact goldberg was only contracted for a year in his wwe stint the first time around that they only used the invasion theme a couple of times before transitioning to the wwe remix.
It'll be telling i suppose what music is used for the match at least. I liked the wwe theme personally, so wouldn't surprise me if they use "invasion" for entrance and the wwe version for exit like they did on raw.