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There has been this weird noise that starts up everytime i play FTL, and i it goes on until i finally quit the game. Its like a prolonged "eeeeeee" sound, anyone else have this problem? How can i fix this? Its less prominent if i turn the volume done but its still pretty annoying.
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Maybe the hamster that powers the ship is making a lot of noise while running in his hamster wheel. Upgrade to newer technology.

Real answer: I had something similar. I think it's the peculiar screen mode that FTL goes into in fullscreen mode. Try running it in a window and see if the sound is still there.