Are you familiar enough with the PCV software to go in and look if it has a enable/disable ACR function? The TTS Mastertune does, but I have no idea about the PCV. Again, that would be the first suspect.
So, to your recollection, the bike was not doing this during the first 1K miles, but started it after adding the pipes and getting the PCV and tune?
Also, you mention a "new battery" in your original post, so the battery has already been replaced in a '10 bike? If so, you're sure the ground connection is good and tight...and clean? A bad ground can cause all sorts of issues and that would be something very easy to check.
The key diagnostic question here is when the problem started showing itself. The early versions of the 110 had some issues with the ACR's, but that has been sorted out for a while now, at least to my knowledge. But that doesn't mean isolated cases can't show themselves.