Hello! I've had the same problem (with KSP 0.90 as well as with KSP 1.0.x) and now I found the reason (and fix) for it, at least in my case: The stutter was caused by the mouse-polling-rate (it was automatically set to 1000Hz on a Logitech G700s). Setting it to 125Hz completely removes the stutter when dragging the mouse right-clicked (I used the Logitech Tool in Windows 7 [Dual-boot] and saved it to the mouse internally). I have no idea how to change the polling rate in Linux without any Logitech driver available (for Archlinux this may help and this for Ubuntu, but these didn't work for me). I came along this solution simply because I play on a laptop with a touchpad. Using the G700s to move the camera or UI-elements (such as mod-buttons) some CPU-cores went up to 100%. The stutter didn't occur when using the pad, but as soon as I used the mouse again, it stuttered. The only difference between the two was the polling rate (80Hz for the touchpad and 1000 Hz, as said, for the G700s). So I changed that and *boom*, it worked.... I commented on the squad-bugtracker (someone else filed this as a bug there without any idea what was causing it) with my system info available there. I hope I could help anybody experiencing the same issue (actually, it's my first post here).