How odd. Have you considered trying an earlier version? 1.6 is almost 10 years old now, and it was always very stable on my mid-end laptop from about that year. It didn't run OOT so well, but Majora's Mask I never had issue with.
I like Project64 the best mostly for its native widescreen support thanks to Jabo's Direct3D. Playing Zelda in 16:9 without having to stretch it is nothing short of amazing.