I believe that while your reader is connected to the computer you have one of two messages on the reader;
- USB connected when the connect SW is not running, and
- Do not disconnect while transferring when the connect SW is running
You may be transferring or not with the second message. Check the Connect SW status. If it is rotating, you are probably transferring. Be aware that the rotation is not continuous but starts & stops during rotation. But if it has been stopped for a while then it should be safe to close the SW & then disconnect the reader.