First off Assume 32bit WAS off by default in the Ini, so you must have changed it or your using a earlier Ini.
Secondly i checked the problem your having (in the same spot your talking about, at the glass shatter) and it played fine with no freeze.
Things to note:
1) Your system is way below spec, and that means you arent or cant run the game at anywhere near full speed, so you will have problems.
2) You stated that this happens with 1964 AND PJ64, AND with any plugin you try, and you also state a few times (without sound) that tells me its NOT an Ini/Rom setting but your system.
I am only pointing out that people with far better systems still have some flashing and other small problems, so if your trying to run it with a way below spec system AND get the same results with other emulators and all other plugins, nothing you do will help much short of getting a better processor and video card.
Until i see people that meet the required system specs having and reporting problems, i dont feel cumfortable changing rom settings that have been working fine all along
Also by shutting off FPU Hack and Link blocks your essentially taking more things offline and gaining that little bit of speed, because thats what you suffer from.