I have the same issue, some of my contacts have multiple numbers, as they sometimes reply using a different SIM card or are in a different country. In Go SMS Pro threads list, they are listed multiple times instead of a single contact. I have checked and I do not have any duplicates in my contacts. I'm using HTC Desire Z updated to Gingerbread and the stock HTC messages app displays them fine (i.e. as a single thread). Has somebody found a solution? Or is it the way Go SMS is designed to work?