OK, here's what my dealer told me to do for a cold start, and it's worked every time. Turn the ignition on, and wait for the pump to stop whirring. Hit the starter for a second or two, then let off. Wait a second, then turn it over again. It should start up almost immediately, run a little rough for a second, then all's well.
Someone told me that this is all due to the vacuum FI system, and though it's fractionally more work to start than my 929, the R1's throttle response makes it more than worth it.