Sorry it took so long, but I finally got it working with the Microsoft WARP driver (using dgvoodoo) with fraps running, and made some recordings.

It seems like normally (for me) the game switches between 60/30/20 FPS and stays stable at those framerates - it seems like the timer is consistent with real time for these framerates (presumably the game runs at the correct speed also). Video:

I haven't been able to record a big lag spike like in some of my time trials yet, but I would assume that when the game drops below 19-20 FPS the desync can happen, giving an apparently faster time.

I did record a bit of lag happening at the start of the level (when you assume control of Buzz), and although most of the lag was I think before the timer started, the audio definitely desynced a bit - seems 1-2 frames behind the no-lag recording relative to the timer, and Buzz seems about 1 frame ahead of the no-lag recording relative to the timer.

I've been taking a look at the differences between NTSC and PAL on emulator/hardware, and it seems as though everything (except audio) is locked to the framerate - the NTSC version runs 20% faster in real time (compare (PAL, I think it's probably on hardware as the channel only plays PAL games), (PAL/PS3) and (NSTC)) - the same happens on PCSXR. This seems to be how it works for Toy Story 2 also. It looks (I have some recordings of running to the bridge in Jo-Ad 2 for PC/PAL/NTSC comparison) like the internal timer is consistent between NTSC and PAL (just running slower in real time on PAL), so I think the only difference is between PC and PS1 (not sure about dreamcast version but looks like it runs like PS1 from some videos I looked up).

I don't know about NTSC/PAL (just checked and my pc disc says "Version 1.0/UK"), but I think it might be to do with lag? In my flamar pb (on pc) I was using the Microsoft WARP software rendering, and it was pretty laggy (does that desync line up with a lag spike?) - I wasn't able to beat it once I switched to GPU rendering.