The feature in Setup to assign a work center to a work station is designed to make it so the user will not have to specify the work center when transferring boards.  If you have more than one work center using that work station, it defeats the purpose and does not work.

If you need to process more than one work station through a computer, then do NOT assign a work center to that work station.  This isn't required to complete the production process, and the user can do it when recording the transaction.