The save games are interchangable between PC versions of the game
GLFrontier is reverse-engineered Atari version with bits of emulator code stuck in and (rather sloppy) GL-support added, aside from true to original display mode.
Saves from GLFrontier won't really work with any other version.
For best experience I'd recommend PC version running in DOSBox (textures, the best colours, least bugs), but do mind that DOSBox itself is rather resource intensive.
As for the shift key, I don't know the source of the problem, but I hazily remember someone else having some similar issue under Vista - using the search function might be fruitful.
If you're desperate you might try slowing down with your main thruster while flying backwards - in fact, putting the ship in "engines-off" (I *so* love this misnomer ) mode, accelerating on full-burn halfway to the target, then flipping your ship so you're facing away from your destination, switching to rear view and decelerating using your main thruster is the fastest possible, (aside from bug exploits), if somewhat demanding and fuel consuming way to get somewhere.
P.S. Switch ship to engines-off mode in combat! With good thruster-work no less-manoeuvrable enemy will ever shake you off, and I'm talking about the "see the type of the missiles they carry" distances here.