I've been having this problem for a while. I already did the usual google searching and didn't find anything useful. Specifically its games I play on kongregate and other sites. When they are using flash player I tend to get poor performance. If it uses a mouse cursor the mouse lags/skips across the flash player window, when it leaves the flash player area the lag doesn't occur. I dont have problems when I'm in games or general responsiveness of the system, I've plenty of space, low processor utilization, low memory utilization, etc etc.
I have windows 8.1, IE11, the latest flash player, video and system drivers are all the latest and greatest. I've found articles suggesting to turn on/off hardware/software gpu acceleration in IE, it also occurs in Firefox.
ideas?