I'm having the same issue and haven't been able to work out. It does seem like an EDID/Handshake issue but since it is not every time I can't pinpoint a cause or solution.
PS3 > 3ft hdmi > matrix > HDMI > Denon 1908 AVR > Sony KDS60-3000A is one path, here form time to time I get no picture at all, just flickering black screens as all things seem to be trying to figure out the correct resolution.
PS3 > 3ft hdmi > matrix > 2x CAT6 STP > cat to hdmi box > 3ft HDMI > LG 42LD520, here I get the black screen cycling in about every 5 seconds.
A power cycle of the main matrix box fixes both issues. I've programmed buttons on my iRule remote to perform the power off, wait 10 seconds, power on, wait 3 seconds and select correct output. But this is a bit of a hassle as powering off the matrix kills what anyone else might be watching in another room.
As I have said, it doesn't happen every time so troubleshooting has been a pain. The PS3 does not seem to care much about EDID, the settings on mine are set to output 7.1 as PCM (have the old 40gig fat) and it does this whether watching on the theater TV with the denon avr in the stream or when just using the TV which has only the TV stereo speakers. So, can't watch a bluray in the living room unless going to the PS3 settings first. Not a big deal, we mainly use it in the living room for netflix, which even with DD the TV can decode to stereo so. Games work well too, mostly just kids stuff and they don't care if they are missing out.
My Dune player is just the opposite. It will only output in stereo no matter which display is viewing as I am sure that the stereo TVs are sending out EDID even when not in use. I can live with this also as I use an HTPC for rips in the theater.
The flickering PS3 is the only thing I really don't want to have to live with. In the grand scheme of things it is not too big of a deal but the WAF of it is low. Every time the little LG NO SIGNAL graphic appears on the TV in the living room my 3 year old daughter sighs, "why is it not working?" repeating what she has heard me say a dozen times.
So, in short, you're not alone but I don't have anything constructive to offer to help you. I am just going to live with it until prices on the better matrices fall a bit, or my finances allow me to splurge on an upgrade.