There's a simple solution to this problem, if you still feel like you need to tweak the visuals/performance (which I recommend, since the shadows etc can be improved a thousand times over compared to the vanilla settings, not to mention all the other useful tweaks). Simply set both the skyrimprefs.ini and skyrim.ini to read only after you're done editing them (right click the files and click the box at the bottom). Then you can start the launcher and it won't automatically force your preferences back to default. Let us know if any other problems arise! Glad to hear you finally got your FPS up, btw!