Yes, you do need to register your pedal with Line 6, along with the amp.

There have been many threads on these forums about Monkey not recognizing the controller.  Standard solutions include trying a different USB port.  What OS are you using?  Windows (version) or Mac? 

I had problems doing the v2.0 update with Vista, but was able to do it on another computer running XP.  Spider Edit (that's what you use for loading tones from customtone.com) works fine for me with Vista.

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