The funny thing is - Stunt Race FX (another Super FX game) runs perfectly - 60fps, no sound pops, nothing - even at 720p. Star Fox you get the frequent sound pop at 720p and Vortex is even worse, while Doom (SuperFX2 game) seems to fare well. I also noticed a bug in Stunt Race FX - before you begin the main race, the dialog screen that pops up is all garbled. So it looks like there are still bugs in SNES9x's SuperFX code.
With regards to the savestates, now with the new compiler it finally explains why the savestate saving/loading causes it to crash - S9xFreezeFromStruct and S9xUnFreezeFromStruct are two functions that the new SDK refuses to compile - I'm going to make a post on the SNES9x Development forums with further details and ask them what changes I would need to make to snapshot.cpp in order to get this working, because this is way out of my league to be screwing around in SNES9x's main code - imagine what I could break .
Just for the record - it will make a huge difference if you're running in 480p mode (there's not much point to 720p mode at the moment) - that, and I've noticed that compiling it with SDK 3.41 seems to do something for the performance, because the sound pops in Jikkyou Oshaberi Parodius are hugely improved - and StarFox/StarFox 2 as well. You'll still notice it with Star Fox 2 - whenever it renders a text/message dialog on top of the game screen, you will hear a slight sound pop - but it's far less bad than 4.3.5 which was compiled with 1.92.