The factory injectors are garbage. (The company is out of business) and a scan wont tell you that they are garbage because unless they fail completely the wont trigger a trouble code.
Marren fuel injection in CT can build you a set of custom injectors cheaper than replacing a single stocker. They built my S-3 injectors. Solved a lot of running issues.
203-267-FUEL. Give em a call...

I have a 99 X1 #170/250 it does same thing when its cold. I put the buell race module still does it took it in and had motor turn apart and found nothing bike runs great when its warm you need to let it warm up it should start to fire