I hope it is not the case, but could it be that the measures to stop save manipulation affect the game stability?
When I played the old version, it ran smooth and I had at no point any issues.
Now the game freezes at every other occasion. For example, when the tutorial for the inventory starts, when a cut-scene starts, when a transition to another location should happen and so on.
And my PC is neither a toaster nor does it have old drivers.
*Edit: Or is it, that the game is set up to be more than an RPGMaker game? I'm not that well versed in it, but is this fancier than other RPGMaker games packaging of the files really helpful for the game.