Re: Quadro FX4800 Display Port Issues On Second Screen
With drivers 195.36.31 and later, the incidence of this problem should be reduced significantly, and the system should no longer get into a state where a monitor connected over a dongle will get "stuck" and restarting X will never bring it back until the monitor is disconnected and reconnected, or the system is rebooted.
How frequently this problem occurs can vary depending on display/dongle combination. I can try to get you contact information for a supplier of Hosiden dongles, or other dongles which should not exhibit this behavior.
I don't think it will necessarily make a difference, but an experiment worth trying might be to connect the real DVI port to the hardware flipping board, and the DP->DVI dongle directly to a display, in case passing through the board affects the timing of hot plug detect cycles or other signals that might affect the operation of DDC on the dongle. If it does happen to help matters, then likely you'll have the left and right images on the wrong monitors; there's an option to reverse this with nvidia-settings, but it needs to be applied every time you start X. (This can be done automatically by putting the appropriate invocation of nvidia-settings in your .xinitrc.)
In the near future, we do plan on allowing explicit configuration of which stereo eye gets displayed on which monitor, so if connecting the dongle directly to a monitor instead of passing it through the flipping card does work around the issue for you, you'll be able to configure X so that stereo is displayed correctly.