I just asked a few guys this same question and figured I'd post this just in case others come across the same issue.
I am using the PC5 auto tune module and o2 sensor on my 2013 250wr/r. I finally uploaded the file provided for my bike and it seems to run better, no popping and the bike initially starts to idle around 1800 rpm, than drops after it warms up to about 1400 rpm. A few questions here, don't know if anything I'm doing is wrong or not. All seems to be working well, bike runs well etc. My question is this, when you guys have the bike running for the allotted 60 seconds (as described in the autotune features selection window) does the "autotune running" indicator light on your screen light up after the 60 seconds? Mine does not light up and I have the on/off box checked in the autotune features checked. No other box is checked. Is this correct? Am I doing something wrong?