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The reason you should bypass the system check when you turn on the key with a cycle that has a piggyback tuner is because it doesn't give the ECM a chance to notice there is a piggyback system connected to it.
The stock ECM will shoot a blast of fuel to the cylinders and choke the air as if it was stock. This allows the engine to fire before the piggyback tuner can start telling lies to the ECM and get the damn thing confused before it has a chance to start the engine.
If you run an aftermarket ECM or a stock ECM with a SERT or SEST you don't have to fret with "tricking" the ECM into starting the engine and can wait for the systems check it goes through while the fuel pump is charging the line.
If you run a piggyback like the Powercommander you should hit the starter as soon as you turn on the ignition.
I never heard that about not waiting for the prime, I do have the power commander V. I will try that tomorrow morning and see how it works. Also the bike will be going in for it's 1000 mile service on Friday, I'll have them look at it.
I had the same problem as you. I checked the cables and they seemed fine but I gave them a quarter turn more and that solved the problem. Check the ground cable on the frame too. Mine also started fine when it was warm, the longer start was only when it was cold.
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