Very interested to see the mention of 16x, 8x, 4x PCIe slots. Is this a verified issue? I have been trying to run 5 x 5850's on a MSI 990 FXA-GD80 M/board with 4GB of Ram. Obviously I am using PCIe extender cables, three 16x and two 1 x 16 extenders. Effectively two  full x16 one x8 and two x1. I am unsure how the M/B allocates the available resources but I doubt the two x16 slots are actually running at that.
All cards are underclocked and undervolted. This hardware setup (under volted and clocked) with CGMiner mines BTC flawlessly, trying to mine LTC at conservative settings gets, in my opinion, way too many rejects and HW errors. I have tried endless settings, nothing seems to clean it up. I had never considered the 1 x 16 extenders may be a problem?

By the way:- great topic, can we get it posted on Litecoin Forum as well? sort of parallel posts or something