Kubota RTV 1100 won't re-start after shut down

My RTV 1100 starts fine when cold and then runs great. But after shutting it off, when I come back to it 15 to 30 minutes later, it won't start and acts like it is vapor or air locked. Doesn't happen every time, but seems to be happening more now than before. I have to crank and crank before one cylinder seems to come on line, then another, and then finally all three. When it does start back up and all three cylinders come on line, it again runs great. It just happened again and I tried bleeding the injector lines, but found no air in the system and it still wouldn't start. I crank so long that I have to let the starter cool off for awhile and today ran the battery low. I've got a clear fuel filter and can see no air at all in the filter. Has anyone ever encountered this problem? Any hints would be greatly appreciated.