I use cinnamon currently and whenever I use ffmpeg to record my screen, blue flashes appear when I interact with the cinnamon panel and applets. When I initiate a recording in vlc, similar things happen but with white flashes instead.
Example recording here. http://youtu.be/bx8xhQmiVBk
EDIT: Tweaked the small applet I use to use avconv, produces the exact same effects as well.
avconv -f pulse -ac 2 -i alsa_output.pci-0000_00_14.2.analog-stereo.monitor -f x11grab -s 1920x1080 -r 30 -qscale 1 -i :0.0 $HOME/Videos/test2.mkv