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The power commander is required to have a 100% perfect crank position sensor SIGNAL.
If the CRANK POSITION SENSOR SIGNAL is not perfect the power commander will have issues and your bike may not start..It can be hit or miss to start.
The sensor itself might be OK but a small nick, cut or slightly loose/bad connection would cause a problem..
Check and recheck the sensor, from motor remove, clean , re-install same sensor then follow wire to connector near battery and open/clean and make sure it is tight and reattach with zip ties then remove connector at ECM and clean both sides, re-clean and re-install...then if everything is good test with power commander...highly likely that something is loose and signal is weak....and make sure to run bike with power commander or you are running lean...once in a while the sensor is bad but it is more rare so do not waste money until all above is checked because a new sensor will do nothing for a dirty ecm connection.
Please read the above, you are running very lean without the power commander and engine damage may result. If you have difficulty or are unsure please show this information to your mechanic. An opened air filter and pipes make the bike extra lean...While the information may not be your solution it is a possibility based on the limited information provided and the inability to see, hear or touch the bike. As mention by others check the pins at the ECM.
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