Now we're getting somewhere. I'll dump this on-list as it's a good example of how to fight this class of performance problems.
The usual troubleshooting procedure is to figure out how the motherboard is mapping all the I/O internally and then try to move things out of the same path. That tells us that you have an Intel S5000PSL motherboard, and the tech specs are at http://support.intel.com/support/motherboards/server/s5000psl/sb/CS-022619.htm
What you want to stare at is the block diagram that's Figure 10, page 27 (usually this isn't in the motherboard documentation, and instead you have to drill down into the chipset documentation to find it). Slots 5 and 6 that have PCI Express x16 connectors (but run at x8 speed) both go straight into the memory hub. Slots 3 and 4, which are x8 but run at x4 speed, go through the I/O controller first. Those should be slower, so if you put a card into there it will have a degraded top-end performance compared to slots 5/6.
Line that up with the layout in Figure 2, page 17, and you should be able to get an idea what the possibilities are for moving the cards around and what the trade-offs involved are. Ideally you'd want both 3Ware cards to be in slots 5+6, but if that's your current configuration you could try moving the less important of the two (maybe the one with less drives) to either slot 3/4 and see if the contention you're seeing drops.
Greg, this is GREAT information and I'm glad you stepped through the process. It is really interesting to see to what extent these slots that have similar names (or the same names) should be expected to behave so differently. We'll try some of the things you suggest (although it will probably take a while to do) and if we come to any conclusions will let everyone know our conclusions.
