What is your monitor type/resolution when this happens? I have had this happen before but it is usually when I have my monitor at 1080p and HDMI boost active.
I use a cheap Element HDMI TV and been playing with my /boot/config.txt options - I have yet to see it happen when it is at 720p
Here are some of the settings I use
# uncomment to force a specific HDMI mode (this will force VGA)
# uncomment to force a HDMI mode rather than DVI. This can make audio work in
# DMT (computer monitor) modes
# uncomment to increase signal to HDMI, if you have interference, blanking, or
# no display