I could never get the Bizhawk M64 reader to get close to finishing runs without quite a lot of desync.
As for this run on Mupen, knowing I'd had it working previously I tried to play it using a few different settings and options and the results were inconsistent. For instance, it'd desync on Glide no matter what I did, then I'd switch to Jabo and it'd sync, then back to Glide and there'd be no issue.
Whilst I'm not sure which of these exact steps is significant, here's the process I took to get it to sync whenever it wasn't working and here's a link the exact build of Mupen I was using (config files included). Make sure to use the correct executable, if you're unsure, it's the one with the blue icon:
https://www.mediafire.com/?bjddzaylczi6jis
I patched Super Mario 64 (U) !: 20b854b239203baf6c961b850a4a51a2
With the patch found here:
http://www.romhacking.net/hacks/1425/
And got this checksum: 15d688de0d23bb437d95c358c635465f
To test and see if the desync is present, go into the graphic plugin settings and set the windowed resolution to as low as possible, make sure "Limit FPS" is off in settings > general and when the run starts, turn off "Dynamic Audio Sync" in the audio options. This will play the run as fast as possible so you can get to the point quicker and is easier for testing it, I find. If you get through a large amount of frames without a desync, you can also make a save state so that you can load it next time and not have to sit through however many frames you successfully got through the first time. When I was testing for desyncs, I just did this every 50,000 or so frames.
If the run doesn't sync with my settings, it could be a computer-specific problem or it could be one of the things I mentioned above. I'd suggest restarting the program and swapping to Jabo's Direct 3D 1.6.1 and seeing if it still occurs. If not, then swap back to Glide and see if there is still a problem.
And lastly, I think if you set the movie to pause at 230728 you'll be just after the reset but before the opening of the next bit, I was testing a 1440p Mupen encode and this is how I did it.
Hopefully I covered everything and didn't trip over what I was saying too much.
Sorry to keep on about an issue I know you're aware of, I'm only posting again because I figured more info may be helpful.
Edit: 
Note that wit the text I didn't set the filtering to automatic because I downloaded a copy of Mupen just for this screenshot, just ignore that.
This wouldn't affect the SD encodes though as they'd be downscaled anyway, it'd be redundant. But it gives anti-aliasing to the insane-resolution encodes!
Without this enhancement:
Both were screenshotted from an AVI I recorded with the program (to ensure it outputs this enhancement). It could be something to consider for the encoder guidelines and I'm sure there's an Nvidia equivalent.
Edit: it functions identically with Mupen and kkapture.