Are you using a pci-e presence detect pin short? With ribbon cables I believe it is necessary, as the ribbon cable is straight through, and the graphics card will not have a 1x short pin hardwired.
If that does not fix it, then you most certainly have crummy riser cables. I notice you have what seems to be extra long versions, right? Most are around 7" long IIRC, or 17cm instead of 24.
Pci-e data signals are differential pair signals, a lot like network cables. They are supposed to carry an exactly 180 degree mirrored signal, in hopes that the noise from each line will cancel each other out. I have a strong personal opinion that ribbon cables are pure garbage, and that as they get longer (or wider, like x4, x8, x16) the crosstalk of the signal pairs starts to degrade the signal to the point that the pc won't boot. Maybe the PC would boot and mine when brand new, but now that things are set up and humming along a lot more electrical interference is getting at those cables, jacking things up now.
There are sometimes settings to open the latency of the pci-e bus, which might help your situation. These are specific to each mobo's bios though, so you'll have to look and try things on your own there.
Other than that, I'd try USB pci-e riser cables. They have individually twisted, shielded pairs for the pci-e data and clock diff. pairs. If it won't mine on usb risers, it won't mine period
