Anyways, FTL would "randomly" crash was was pretty annoying.
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*** Error in `/home/user/.steam/steam/steamapps/common/FTL Faster Than Light/data/amd64/bin/FTL': double free or corruption (!prev): 0x0000000000d5c8d0 ***
In "/etc/pulse/daemon.conf" I uncommented
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default-fragment-size-msec = 5
And game appears to have stopped crashing as well as the flashing is gone.