I downloaded the latest beta from the website.
I've only tried RE4 and MGS2, because those are the only two games I have interest in playing again. Getting a game for PS2 takes a bit longer to download (especially if you have to manually download each individual part from like Megaupload or something) so I haven't really snagged random games to try out.
Pretty sure it's not an overheating issue too. The slowdown occurs as soon as gameplay starts, even if I skip the opening cutscenes. Just to be sure I checked with Speedfan and my core temp doesn't go over 40C.
Edit: So I noticed the fps counter at the top of the pcsx2 window. Apparently I can maintain 60 fps fine in menus and cutscenes, but when actually playing this is reduced to 30-45 fps in both RE4 and MGS2. Sounds like a decent amount of frames but the slowdown is still noticeable and annoying, but is that "normal"?