Strange. I naturally assumed that it would be the HDMI socket that has this issue.
Did a little digging and found this by Mr Grand Bennett. It was here: https://discussions.apple.com/thread/2746930?start=0&tstart=0
A related topic, but the same fundamental issues is being discussed nearby:
The movie version is that Mini DisplayPort does not convert directly to DVI, and the card cannot run three displays reliably unless you are using ACTIVE or POWERED adapters to convert to HDMI or DVI, which provide active conversion.
This is not your Mac Pro model, but you ARE using its display card, so these DO apply:
I already have this setup the Resolution paragraph is speaking of.
I am using 2 Mini DisplayPort to Dual-Link DVI Adapter from Apple. One of the USB power sources is plugged into the computer and the other is in a USB outlet on a power strip. The third monitor goes straight into the DVI port on the card.
"If you use three displays, you should connect at least two of them with a Mini DisplayPort. You can also use the Apple Mini DisplayPort to Dual-Link DVI adapter or the Apple Mini DisplayPort to VGA adapter or just connect the devices to the graphics card using their native Mini DisplayPort connectors."
I blundered onto this article and thought of you. I am not sure it applies, but maybe it will jar someone's memory:
In certain situations when you use Windows software under Boot Camp on a Mac Pro, the display may remain at 640x480 resolution (4-bit mode). Selecting other resolutions may have no effect.
To use resolutions other than 640x480, you need at least two gigabytes (GB) of RAM installed in your Mac Pro.