Maybe you already established this but I would suggest as a rule for now to not bring up PCM audio sync issues in the compatibility list, as they seem to show up in every game. Its more noticable when the music combines PCM and gameboy audio, but again as it seems to happen to every one that uses that, not sure if its worth mentioning over and over. Then again I'm noticing white noise in place of the explosions in Metroid Zero Mission and the cause could be sync related for all I know.
Also a note, it looks like the "timing issues" from using main memory cache option can be exacerbated when running at 133 mhz. Like in the FFVI opening credits, showing the mechs march in 3D snow, runs at almost double speed. So maybe another reason to treat 66 mhz as the baseline.
And when I launched Sonic Advance / 2 I'm getting grey rounded bars instead of the game. I thought this was caused by the link cable not being emulated, and you added this feature recently?