That's frustrating, stinger. You say you have a Rexxer flash on your ECU - did the starting problems coincide with the reflash?
I'd have thought if you had a problem with one of your sensors you'd get a fault code but you say there are none. But I wonder if the ECU is getting a false temperature reading when you try to start it. With my Rexxer flash, I got the ability to see the Intake Air Temperature (IAT) sensor reading on the dash - do you have that too? If so, the temperature reading you see before a cold start should be close to the ambient air temperature. If the reading differs considerably from ambient, it may indicate a problem with the IAT sensor. (The sensor is no. 6 on the diagram.)
You could try disconnecting the battery overnight to purge the ECU. Be aware that it may initially actually run rougher after this until the ECU relearns all the autoadaptive parameters, (perhaps a couple-of-hundred miles).
A hot TPS reset might be worth a try too. If you've not seen this before, it involves starting the bike from cold and allowing it to run
without touching the throttle until it shows three bars on the temperature gauge, then turn the motor off. (That should have been done after refitting the reflashed ECU.)
For cold starting, the 1100 employs a stepper motor, (no. 14 on the diagram). The effect of the stepper motor is the same as opening the throttle so you could try a cold start with just a hint of throttle and see if that improves things. If it does, it may suggest a problem with the stepper motor itself.
