notaz, I honestly don't really know what happened as I was trying to find a common thread between the problems, but they play fine now. FFVII wasn't overclocked to more than 700mhz, but it was very jumpy right after the opening cut scene, and now it plays fine. I almost never clock that high, and my default is 600mhz with frameskip ON. After posting that, I compared the config files from r6 and a newly-generated one from r7 and noticed they were identical, so obviously it wasn't that. Same disc image, but suddenly FFVII played smoothly. It was late as I was trying this, so perhaps I did something that I wasn't aware of, but I cannot recall any one specific thing that I did that made the games run better. I had already tried rebooting as well and the errors persisted. Perhaps something funky on the SD card? Not sure.
The only problem I keep getting now is the memcard issue.