Hi Sun --
Part of the points being lower is likely as BAP said, I think we were in the 762x onslaught when you got them going and the points drop thereafter would not be termed outlandish but it was certainly more than noticeable. By sheer coincidence I just happen to have one on one of my cards right now, but they're infrequent.
The 3D to 2D thing is a greater opportunity because it's one that can usually be addressed. It's almost always the card protecting itself from heat. How are your temps? Got a fan you can blow at the system and see if it makes a diff, just to confirm that it's heat? The other thing that if it happens and you don't re-boot, (as you have) it will stay in 2D until you do. When you do and it returns to 3D and then subsequently drops again that tells me it's probably heat. You could also try merely removing the side of the case as well but let's get a heat benchmark first. Just use MSI AfterBurner if you need a utility, you can adjust a bunch of other things with it as well.
Everybody else continue to jump in, I'll be missing stuff. Start there though Sun.