Screen flashing

[sinknode]

Hi, my emulator has been going great so far with the exception of one thing, when I go into the save screen or some menu screens (I've observed the save function to be associated with these menu's) The screen goes manic in flashing. It isn't damaging to the performance and luckily I don't have photo epilepsy or there would have been major bad.

Just wondering if this is a common problem and if there is a solution to it?

Thanks,

OS: Linux Mint 17.2
Input: PS3 controller via terminal commands "sixad -start" for connection and "jstest /dev/input/jsx" for calibration.
Currently playing games: Wipeout Pure (only experience it when loading profile.) and the Legend of Heroes: Trials in the Sky (experience it when both loading profiles and on the in game menu screens)