Not sure EXACTLY what you're saying,but it sounds like an installation problem.Maybe you'll have to go through the Smartlink Software Removal programme as outlined in the Smartlink manual.
I loaded the Smartlink programme into my laptop so i could just take it out to the garage and hook straight to the bike.I also downloaded the Smartlink Manual in pdf format and printed out,and bound the whole thing.Makes a great and EASY reference when you're hooked to the bike and don't have to toggle between windows.