PCIe MADI card noise related to FireWire bus?

I've recently added an SSL MADIXtreme PCIe card to my Mac Pro 2,1, and experience noise interference that is embedded in the digital audio stream, prior to it reaching my D/A converters. It is more prominent when operating at 96k. The noise is not a clicking that you would normally associate with clocking issues, nor is it like an aliased signal that you get if the MADI stream of the interface (Alpha Link) and MADI card are misaligned i.e. one is in 56ch mode and the other 64ch mode.

After trying different clocking schemes e.g. external word clock vs clocking from MADI and either way around (interface to card, card to interface) etc. I swapped the card, all cables and the interface for multiple other units. I've also pulled out all four hard drives (boot from an additional SSD) and any other PCIe cards (firewire) except the graphics card, and still no change to the fault condition. The symptom is the same when running multiple different DAW packages, e.g. Pro Tools and Logic, using a signal generator in each case, and Ive tried rolling back to Yosemite instead of El Capitan. The equipment has been proven good with other Mac Pro systems, but they are much newer.

The only thing that has any bearing is the firewire bus; I have the old 23" Cinema display with the USB and firewire hub/breakouts built in, so there is a firewire cable normally in the motherboard's rear port. Plugging or unplugging a cable in here (e.g. the display's, even though there is nothing on the other end) temporarily cures the noise for a couple of seconds. This works both when adding or removing. While this is happening, it is inconsequential whether the display DVI is actually connected, or the display even plugged into mains. Audio still passes the entire time, but the scratchy interference miraculously disappears.

My conclusion is that there is some errant noise from the power supply and/or from the firewire bus that is getting into the power rails for the PCIe bus, and this is somehow interrupted when the firewire bus is somehow made active by plugging/unplugging. Mains distribution has been moved around wth no change (e.g. removing other equipment from the ring main, and trying with/without various mains filters and at different wall sockets.I have no idea how to troubleshoot this further - is this just a failing motherboard / power supply / other? Has anyone else had a similar issue? Any comments or speculation much appreciated. I'm no stranger to grabbing a multimeter, so if there are some reliable test points and voltages to check, I'm all ears.

I remember when I first got the machine (back in July 2007!) I ran into problems putting a firewire interface on the built-in in ports, especially when I had a firewire HD on there as well, so I got a PCIe firewire card and that was fine. That is the only other experience I can relate back to.