Z77A - GD65 - tricky one problem with 1X and 16x mix.

Question

I can tell you some feedback that I have done extensive testing on - ANY help would be greatly Appreaciated !
(if you have a digital wallet of particular happy to send Crypt cunnency ! for solution ! )
I have 6 7900 Series ATI for sCrypt mining  using CGminer  but all that aside i think this is a PCie problem?
on our MSI Z77a_GD65 - if a 1X and a 16X slot are connected the  16X slot get allocated GPU 0 in CGminer and by default sets to 500MHz Core and 150Mhz mem clock. i.e it does not function properly -
its like the plugging in of a card to the 1X slot is voltage down the 16X pcie slot - or taking Channel space from it?
This board has 6 usable slots - if 3 Cards are in 3 1X slots then all will # at around 550 500 K# without tweaking no problems , everything is normal .
likewise if 3 Cards are in 16X size slots - all cards Run  , 3 cards run  fine .
BUT
if slots are mixed - even just 2 cards  i.e 1 Card on a 1X and 1 Card on a 16X  - then CGminer sets GPU 0 to the the card present in the 16X slot and sets it to 500mhz Core and 150Mhz memclock .
I've tested multiple combinations of 1X and 16X slots so as to exclude any particular slot  i.e 1 and say 5 and 3 and 2 .
Also updated Bios to 10.8 which states "better Pcie Compatibility"
Set PCIe Latency to 96 in Bios.
danced around room with wooden totum , sacraficed a rubber chicken.
Disabled Gen3 becasue it is not needed - Cyrpt mining does not need bandwith.
looking for the answer, maybe a voltage issue?
may result in jumper or Pin?
power is ample have 1500W Revo _ and this happens when running just 2 cards.
8 Gig Ram - Processor INTEL G1610 - should have enough PCI channels ?
Driver 13.5 - SDK 2.6 - not a Driver problem tried nearly all drivers.
PCIe Problem !? voltage issue?
** also any card run singally by itself in any single 1X or 16X slot is fine and performs normally.
I purcahsed the Motherboard New and it still has Warranty.  (other than that love the booard, love the onboard IO button)

Answer 1

 The Intel X79 Express platform supports 40 PCIe 3.0 lanes via the CPU for graphics. The Intel X79 Express PCH itself supports eight lanes of PCIe 2.0 connectivity for other external devices.
 Of that would also require purchase of Sandy-E CPU along with the BB-XP ll
 Compare that with the much less 16 lanes for Sandy & Ivy platforms.
 It's not an issue of how many cards you use, it's how many lanes each card uses. If you use 3 cards that use up all lanes and have empty slots they are useless anyway because you have already used up all available lanes.