What model Mac Pro?
What OS versions?
What GPU? How is it powered?
What are your system OS drive(s) and formats? HDD, SATA SSD, SATA SSD via PCIe, NVMe SSD via PCIe?
When was the last time the battery on board was replaced?
Is this an authentic 5,1 or a 4,1>5,1?
What firmware (boot rom) are you on?
I'd suggest replacing the 3V coin battery on the board. This is BR2032 as OEM. The CR2032 batteries work and are usually easier to find locally at retail locations, but they do not last as long. This is a very cheap and easy replacement to begin to troubleshoot the issue.
I had this issue. Turned out to be the no-name USB 3.0 card I had installed. When I moved to a Sonnet card, the problem went away. I'd try yanking all possible PCIe cards other than preferably a EFI GPU and jamming them back in one at a time.
When you yank the card, you may want to reset the PRRAM, although if memory serves me correctly, this means if you're using an NVidia card you'll deal with the drivers. In any case, I thought I recalled my Mac Pro doing the same before, but yanking the USB 3.0 card was the key. I was only out $17 or whatever I paid for it.If so i need to try it, hope it doesnt :/ but i remember it was doing the same when the card was out. Will try it again.