I'm very early on in the game, but noticed something odd about the way the game is handling saves. It seems like it just can't override saves, so I can only save once per area. So for example I made a save in the vent when first going into the hangar, and then no matter how many times I save again and the game will tell me it's overwriting an old save (and doesn't give the option to just save in a new slot even), if I load that save back up then I'm back in the vent with the equipment I had when I made that first save. So if in this example I go pick up the thermal goggles, try to save, and then load my hangar save that is supposed to be overwritten, I'll load to be in the vent and without the thermals. But it has no problem making that first save in each area, so I'm assuming it is the overwriting of saves that's not working.

I've only played a little bit of MGS on Playstation, but I don't remember it working like this, Is there some kind of setting in Galaxy/Windows that I might be missing that's making the game act like this? I know the GOG store page says it's added quicksaving but I've not touched that as far as I know, so don't think it shouid be interfering.

This is working as intended and was like that on Playstation as well (As well as all the games that came after this one.), Whenever you enter a new floor or area, the game creates a checkpoint and if you save, that last checkpoint is exactly what the game saves. You can't save any half-way progress you've made on a floor, you have to create a new checkpoint first by going to another area.

Edit: Okay, re-reading your post it says it loaded you into the vent again. That's indeed a little bit strange, it should've put you right at the point where you left the vents if you've saved anywhere in the tank hangar.