Did you install latest BSP versions? we are suspecting maybe older BSP versions would cause this problem?
Could you share which BSP and Workspace you are downloaded and used?
Could you try once again step by step instructions as described here : http://www.toradex.com/community/answers/32348/view.html to build the image and let us know if you are gettting the same problem?
Also, we would like to know why do want to build the image? Are you trying to add or remove any features from WinCE image? If so, please let us know some more details about that.