Alright, I cued up Steel Gear once again. The run-through went like normal, until I started noticing weird things happening.
First, in Building 2, I was able to move through some steel drums and a crate in the room on the right-hand side of the building near the sludge pool. OK, whatever, it's a minor graphical glitch in an out-of-the-way part of the building, so no biggie.
Then I was able to use the ladder for the walkway around the sludge pool to actually get on top of the walkway, surprisingly. I got back down to the floor surface, things seemed to go like normal again.
Then once I got card 8, I went back to the beginning area to open up that storehouse and build up my ammo reserves. There, I started noticing that as I was killing guards around the storehouse with the sniper rifle, they weren't always doing the "!" thing as they died. Even weirder, sometimes they'd do it *after* they died, once even when there was just a bloodstain on the ground. The alert music continued while I went back into the storehouse, then came back out, and didn't revert to the normal music until I killed another guard. Weird, things are seeming gradually glitchier as time goes on, but it's still generally going OK.
Then I got to the supercomputer room, entered the code to Steel Gear, that door opened up, cool. While I was in there, I wanted to use the console, so I tried hitting the "0" key; nothing happened. Tried several times, still nothing. OK, whatever, I didn't really have a pressing need to use the console. So I went ahead and destroyed Steel Gear, the countdown started, I headed into the room with the Big Boss in it, but for some reason while the cutscene was playing, I was idly pushing keys on the keyboard waiting for the cutscene to end, when I noticed the sound effects for firing the sniper rifle, and opening/closing the door. As if I was actually moving the character around, though I couldn't see what exactly it was doing since the cutscene was still going. Then once the cutscene ended, the game window went completely black, though the music and sound effects continued just as if I was playing the game (including the sfx being timed with keypresses), but I just couldn't see anything, it was completely black. So I had to quit the game at that point.
Sorry for the wall of text, but I really have no idea what went wrong this time. Maybe some kind of working memory corruption or something? I don't know what could cause the game to get gradually glitchier like that. If you need more info, please let me know and I'll add whatever I can to help you figure this out.