If it was me I'd try the cards one by one, if all work like normal on their own then I would suspect the PSU/s. Which PSU's do you have?
I did go ahead and test individually with cards, using different pci-e ports, with/without risers, etc.
My PSU's are here:
http://www.newegg.com/Product/Product.aspx?Item=N82E16817190033http://www.newegg.com/Product/Product.aspx?Item=N82E16817182188The rosewill is the primary so it runs the system, hdd, and 1 card
the xion runs 2 cards
I don't think the psu's are being pushed to hards, but that doesn't mean they could be bad i guess. Total wattage with the 3 cards was around 1300 watts.
edit
I went ahead and ordered a new mobo so we'll see how that goes.