I was really annoyed that I had to put the Intel Quad Port PRO/1000PT right next to the video card in my new build since it wouldn't work in a PCI-E 3.0 slot - and, in fact, would stop the machine from booting if inserted. That was making the video card 5-10C hotter since it was passively cooled and needed a bit of air circulation.
So I dove into the BIOS and found that I could set the PCI-E version for the PCI-E 3.0 slots (but not the 2.0 slot for some reason). This could be just the thing - so I set the problematic PCI-E slot to PCi-E 2.0 mode, remembering that Supermicro still numbers the slots as if the PCI-X slots that aren't there on the X9SRI are still there, and moved the network card over. Lo and behold! The machine booted.
Unfortunately, this was as a result of the network card just not working at all, as opposed to actively stopping the boot process. Obviously there is a subtle difference between a PCI-E 2.0 slot and a PCI-E 3.0 in 2.0 mode - remember, this is an Intel network card in a motherboard with an Intel CPU and chipset. Moderately unimpressed with both Intel and the mess that seems to be PCI-E standards.
A search for Intel documentation reveals that the low profile PT-cards are actually PCI-E 1.0a (which I wasn't aware even existed) which should work with PCI-E 2.0. Finding this was a lot harder than in the past as Intel seem to have expunged or broken links for older products. I remember when they used to have really good legacy support not so long ago (i.e. 18 months!). So I drop down to PCI-E 1.0 in the BIOS and finally everything works OK.
Outcome, a cooler, working system and increased disillusionment with Intel and the whole PCI-E mess. PCI/PCI-66/PCI-X either inter-operated or was keyed so you couldn't make a broken configuration - this is not progress, guys!
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