I had some concerns myself as to the value of repurchasing the game from GOG since I already own the CD version, however, I figured 5.99$ isn't too much to "waste" and the payoff is potentially great:
1. No DOSBox is involved, this is a windows game
2. the GOG version (1.04) does indeed solve the audio skipping problem... installing the original CD version, applying the registry patch, and the 1.04 patch from valkery studios did not solve it, so the GOG version does provide added value.
3. Neither version will play the cinematics as is on windows 7 64bit. After installing a bunch of codecs (not mentioned anywhere). including FFDShow and quicktime alternative, I had to set the septerra EXE program to run in windows XP SP3 compatibility mode for the FMV to show up.
bottom line, the GOG version of septerra core includes extra fixes that don't exist elsewhere and is worth the money, even if you already own the CD version.