Why are 2 Mac Pros on a separate subnet directly connected seeing very low transfer rates?
My first guess would be the crossover cable you're using to connect them. Gigabit ethernet requires a different crossover wiring than 10- or 100-megabit ethernet, and if you have the wrong kind, the computers will either figure out the problem and switch to a slower connection, or just get massive amounts of errors. I don't have 2 Mac Pros handy to check myself, but you can check this in the Network Utility's Info pane: Select the relevant interface from the pop-up menu, then check the Link Speed listed on the left, and the error counts on the right.

If this is the problem, I'm pretty sure the fix is easy too: just use a straight-through CAT-5 (or 5e or 6) cable instead. Pretty much all modern network interfaces do auto-MDIX meaning that the interface can do the crossover internally. Again, I don't have Mac Pros handy to test, but I'm pretty sure their ethernet interfaces support this.