I didn't have that issue when I installed the driver, but to be safe I would play through with a vanilla installation and save your first save once in each of the ten memory slots.
Also, if you want to use graphical mods I know the Team Avalanche mod is stable with the driver, and in fact requires it. You can find that
here. That one gives you updated world graphics, and comes with an updated Barrett model and texture. As for other character replacements, most anything else you'll find aren't technically legal. However if you're willing to wait I know APZ Freak is working on a new cannon specific Cloud model, you can keep an eye on the project
here.