Here is how I fixed my PCi-e x1 problem. I was trying to decide if I wanted to run my memory at 1:1 or 4:5. When I had it at 1:1 my PCi-e was x1. When I changed it to 4:5 the PCi-e was x16. I flipped back and forth a few times and the results were the same. I tried changing the NB vCore and it was not the problem.

P5B Deluxe (Bios 1101)
e6600....389 FSB running at 3.51Ghz
Sapphire X1950Pro 512MB
2X1Gb G.Skill F2-6400PHU2-2GBHZ (4:5) running at 973Mhz (4-4-4-10)
vMemory: 2.30
CPU vCore: 1.4625
FSB vCore: Auto
NB vCore: 1.55
Sb Vcore: 1.50
ICH vCore: Auto

PS: I tried for 400 FSB with a vMemory of 2.40 and the bios page froze. I thought I was done. It would not post on repeated tries. I had 4x1Gb of memory, so I tried one set at a time and sure enough one of my sets were defective and would not post. So I guess 2.40 volts is not good for this memory. I am glad I had two sets of memory or else I would not have been able to figure this out. I RMA'd the memory and I am going to keep it as backup from now on.