I mentioned the same problem with Cubase 8 here: (mine is 3rd post from the bottom.)
Once I unticked everything and then just ticked the one folder I needed my performance went way up. I think the Cubase 8 install resets everything to default and it wants to search your c: drive.
Switching Media Bay off helped with the GUI lag I was experiencing when zooming vertically in/out (would always hang for a second as the zoom handle passed near the halfway point). So weird that one would affect the other!
Hasn’t cured it completely, but has cut the stutter down to less than half a second.