Can only boot with 2 cards?

[Starcraftman]

First of all here is some information that should help. I am currently running windows 7 premium 64 bit. The motherboard is a MSI 880G-E45, and I have used it to run 3 5830's in the past when running win XP 32 bit. The PCI-e slots are arranged as follows: 16x(runs at 1x because I tried using tape to force it to 1x), 1x (covered by 1st card), 1x(PCIe x1 extender attached to this), 1x(back cut out to allow 2nd card to be inserted onto mobo). The only real difference between this setup and when it was running XP is that when it was running XP the first 3 PCIe slots were all occupied by pciex1 extenders, leaving the 4th slot empty, but now the first, third, and fourth slot are occupied. When I try to boot up with a card attached to the 3rd slot via extender cable, the computer freezes at the windows boot screen, restarts, and then the bios says that a Hyper Transport Sync Flood Error has occurred. I don't know if it makes any difference, but the PCIEx16 slot is a 2.0 slot and I assume the x1 slots are all PCIE 1.0 because they are not listed as 2.0 in GPU-z, like the 16x slot is.

What works:
-Booting up in safe mode
-Booting up WITHOUT GPU drivers installed
-Booting up with PCI lock enabled, only 1st card works but the other two are detected with errors according to device manager
-Booting up with card removed from the 3rd slot
-All the GPUs work, I have tested them individually.
-I used tape on the card in the 16x slot to limit it to 1x

What I have tried that does not work/does nothing:
-Disabling clock frequencies to unused PCI slots
-Using the onboard GPU as primary
-Changing PCI latency timer
-Changing all clock frequencies in the bios to default values
-No GUI boot
-Booting without dummy plugs
-ATI drivers versions 11.5, 11.6, 11.8
-THERE IS NO BIOS UPDATE FOR THIS BOARD

I spent hours trying to fix this today, and I am totally out of ideas. Any kind of suggestion would be great.
Sorry if this is the wrong section, but I cant create topics anywhere else.

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[niko]

Would you mind explaining the tape detail? What exactly did you tape and why?

[Starcraftman]

I covered the pins on the graphics card to force the card to run at 1x bandwidth while inserted into the 16x slot. My reason for doing this was because I thought that perhaps running that one card at 16x was using too many of the available pcie lanes. Either way, doing this made no difference to fix the problem.

[niko]

If you haven't solved the problem yet, here are some thoughts:

- according to Wiki, systems with on-board GPU often cause trouble -- https://en.bitcoin.it/wiki/Mining_rig#Tips
- try different versions of GPU drivers; it's symptomatic that the rig worked under xp
- try updating BIOS

[Starcraftman]

I have tried running it with the onbaord GPU enabled/disabled and that does nothing. I wasn't aware that just having an onboard GPU could cause problems, and at the moment I don't have the option of using a different motherboard. I have already tried 3 versions of ATI's drivers, 11.5, 11.6, and 11.8. There is no bios update available for this motherboard.

[Starcraftman]

Ok turns out it was a faulty PCIe extender.