Hi Hank,
Since we have not released WINCE7.0 BSP for i.MX6, we have no better suggestions for you.
From your description, in the Linux environment, both USB ports can recognize your USB device, but WINCE7.0 BSP cannot recognize one of them, so the best way is to contact the WINCE 7.0 BSP provider to obtain More help.
Have a nice day!
B.R,
Weidong