Well, this is not a Jabo's gfx plugin bug, because this doesn't occur in 1964. There's definitely a core bug in PJ64.
Here's one of the Harvest Moon 64 slowdown spots:???
With Snowboard Kids (1) in PJ64 1.2, even when the game is running full speed, the VIs are only in the high 40s to 50s.
You will notice this in the screenshot.
This is Snowboard Kids (U) [!]