I have an issue where my 2003 R1 will bump start easily, but will not start otherwise. Battery is fully charged, and terminals are good. Once the bike is running (after bumping), there hasn't been any problems. When I turn the bike on it cycles through it's power up procedure, and sound like it's healthy.
I've noticed that if I go for a decent ride (>1.5 hours), and get the bike fairly warmed up, that if I stop for a bit (e.g., 10 mintues), the bike will start up again, sometimes. But if I wait for a day after shutting the bike down, it requires a bump start to get it going again.