You should definintely update your phone to iOS 6 regardless of the Wadia issue. I'm not sure what app you are using for notes, but mine always back up without issue.
Your problem might not be a pin on the dock. It could also be a pin on your phone, or some dirt or debris. Try cleaning out the connection on your phone. Also, does the phone work with any other dock accessories?
Your problem might not be a pin on the dock. It could also be a pin on your phone, or some dirt or debris. Try cleaning out the connection on your phone. Also, does the phone work with any other dock accessories?