Yep. I've had the very same problem. Very embarrassing when you're being paid to do a presentation and your brand new, top of the line retina macbook has a temper tantrum.
This happened to me at 3 different venues with three different HDMI external monitor/projector set ups.
To fix this each time, I restarted the mac with the HDMI inserted. I quickly got to the system preferences>displays window... Turned off mirroring; and reset the resolution of the mac monitor back to full res... and the external monitor down to a lower res and refresh rate.
The mac seemed to need a minute to think about it before it came good.
Perhaps something about the HDMI "confuses" the mac as to what monitor is what.
This has never happened to me using VGA.
It could be the whole HDCP encryption "handshake" thing? I'm not sure.
As well as this, I also got occasional random dropouts to "digital snow". One even caused the macbook to crash and freeze... Requiring a full restart.
On another occasion I was using a supplied Mini display port to HDMI adapter... and was getting dropouts with that.
The VGA via mini display port is stable and runs all day long... The HDMI output now officially frightens me.
A lot more venues are starting to use it.