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PC doesn't do anything directly to the ECU. PC takes the signal coming from the ECU to the injectors, intercepts it and modifies it to be either richer or leaner.
The fuel map you have installed on the PC might not be right. Instead of pulling it out, I would just load a null (no change) map and see what that does. That would be like running it with the PC removed. You can find the null map at the power commander web site. Another thing could be that you have the right PC map installed, but the three manual adjustment buttons on the PC unit map be messing things up. Return them to neutral and see if that helps.
A power commander map is usually made specifically for a bike from a dyno run. If you don't do that or can't afford it, then you need to use a downloaded map from the internet and tweak it with the power commander software. I found a map on the internet for my daytona and pipe, but did significant modification to it in order to get things to run smooth.
It is worth spending some time to figure it out. Makes a world of difference in power delivery and smoothness, especially if you have an aftermarket pipe and air filter.
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ROWYKO!
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