I'm not a mechanic but I wonder if this model has a lambda sensor, did I spell that right? If it does then maybe this could be the fault. This is a question to the more knowledgeable on here rsitch, someone will answer soon then we'll both know the answer.
You said you are starting to experience this problem. Did the bike run properly with these aftermarket things fitted when you bought it? Is it possible to ask the seller if he/she could throw any light on the subject?
Another thing that came to mind is, as the aftermarket can was fitted before you purchased the bike, were you given the original can too and if so, why not fit it then disconnect the power commander and see how it goes then?
Good luck with it anyway and don't forget to let us know what the fault was when you know.