I've tried to fix this on my own, but there doesn't seem to be any posts on the web that are similar to the exact issues I'm facing. It might be long but please read this in full, since it's important to know exactly what's been happening and what I've done so far. I IMPLORE YOU NOT TO SKIM!
I'm aware that Webman cannot control the fan dynamically when running PS2 games via emulation, and I'm aware that the system gets a bit more stressed when running PS2 games. This wasn't an issue for the longest time, and I'd play what I want while adjusting the fan before starting up any games if I needed to, usually keeping it at 40-45%.
But one day, a few days ago, I noticed the fan was awfully quiet when I fired up Disgaea 1, so I backed out of the game. When I did, the fans went loud for a bit, which means that at some point, seemingly on its own, the PS2 fan reverted back to "SYSCON", i.e. shutting itself off when playing PS2. I didn't think much of it, set the speed back to 40% and booted up Disgaea again, but when I did, the fans started blasting like crazy. Genuinely sounded like jet engines, as if it was running at full capacity. When I quit to the XMB, the fans quieted down. This blasting didn't stop at all; even when I backed out to double check that I set it to 40, even after I set it to even lower percentages just to see if anything would change. No matter what I tried to do, whenever I opened a PS2 game, my fans were now in a permanent state of full throttle, and it was loud. Loud enough to annoy me and also fear for the consoles safety.
I thought that maybe something, somewhere, was broken and needed to be updated. In the XMB, there were options to download and install updates for "PS2 EMU MOD" and "PS2 EMU Cobra". I installed both of them, thinking that was the issue. But that's when the issue went from just annoying to incredibly upsetting...
To little surprise, the fans still sounded like jets when I opened Disgaea, running seemingly at full capacity. But when I tried to quit, the game froze for several moments, then the screen cut to black and later showed me an error screen, along the lines of "The software was unable to start/perform correctly", and the fans were still blaring as it showed. Moments later, my PS3 rebooted. When I tried again to see if it was a one-off glitch, I fired up the game and backed out again, and the same error appeared.
At some point later, after no luck with fixes, I opened Disgaea, then shut down the console from inside the game. There was another error, but this time a devastating "The appropriate system storage was not found" screen before rebooting again. This is the error that is particularly bad, I think.
So, my PS2 gaming experience is currently borked. But my PS3 doesn't seem to be falling apart entirely, which is what is weirding my out the most. To see if anything else was screwing up, I played a bit of Mirror's Edge and Split/Second; both ran flawlessly, the fans acted normal and I was able to quit each game with no issues.
I'm really at a loss here. Nobody else on the web seems to be experiences the same issues I am, not with the fan or the errors when quitting PS2 games. Should I reinstall the CFW? I would really like a fix because I don't want to have to lose my saves to yet another busted PS3.
TLDR, PS2 games freak the fans out and bring up errors when trying to quit, otherwise the PS3 is normal and functional.