Sparkfun has finished looking into the problem, and it sounds like they are not going to do anything about it. We have put a warning on our page for the Arduino, but there is not much more we can do, either.
After looking into the design, it seems to us that the circuit is just fundamentally flawed, and there is little reason to expect it to work well regardless of which MOSFET is used. The newer MOSFET makes the problem more evident, so it is easily verifiable in all kinds of tests. (These were not just contrived tests: on the one laptop we tried, we measured almost 200mA flowing into the USB port after powering it off. We verified that this occurred across the entire recommended operating range of 7-12V on VIN.) The new Arduino Uno looks like it will have the same basic problem, but we have not tried one yet.
While we do not know of any cases of damage to computers, 200mA is not a trivial amount of current, so we do not recommend leaving an externally-powered Arduino connected to your computer, especially while the computer is off.