Ok, here's the situation: I have an Ultegra 6600 crankset (2007, 10-speed) on a Soma Double Cross. I'm using a 9-speed Dura-Ace FD, a medium-cage XT rear derailleur, and a 9-speed SRAM cassette (11-28, I think) and a 9-speed SRAM chain.
The problem is that when the chain is on the little ring up front, on the smallest 3 or 4 cogs in the rear it wants to upshift to the big ring up front. The chainline presses it against the shifting ramps on the big ring and so it skips up.
As I see it, there are 2 potential problems. The first is that the front part of the chainline is just a little too far towards the center of the bike, so the chain angles outward enough to hit the ramps in the lower gears. The other is simply that the 9-speed chain is too wide (despite what a lot of people say about crankset compatibility across 9 and 10 speeds) and a 10-speed chain wouldn't perform this way.
I can get a small BB spacer and try to move the chainline out a little bit, or I can try a 10-speed chain, which I suspect won't work on the cassette. The expensive and painful alternative is to find a 9-speed crank, but I hope I don't have to do that as I like the Octalink II setup and also, heck, I've already got the 10-speeder.