Sounds like you are using an older video plugin you should take the time to report these issues on github
https://github.com/project64/project64
I would test with a few different plugins to see which works best for each game you play. If you want accuracy I would recommend hatcat's RDP/RSP, but its really slow. If you want decent accuracy, with moderate speed I recommend GLideN64 RDP.
Anyway, I see that you are claiming to be a supporter. PM Zilmar, and I think he will give you access to the beta builds. There is also Patreon support available if you want to support the site, and zilmars goals.
https://www.patreon.com/Project64/posts