R6 2003 cutting out!

Hi there,

I have a 2003 R6 and had the TPS (throttle position sensor) changed about 3 months ago, I fitted a power commander and used one of the maps from the web, the bike has been running fine for around 2 months, last weekend went for a blast and the bike kept cutting out but only when I stopped at traffic lights, so basically no idle whatsoever, when I switched the ignition off and then on again the bike ran fine for a few hours then did it again, is it possible that the power commander is causing this problem? because I haven't had a custom map created specifically for my bike? also I used super unleaded petrol a couple of times while out due to the garages in the sticks not having normal, could this cause a problem? Someone told me your only really supposed to use super unleaded 1-4 with normal unleaded, is this true?

Thanks in advance