Can you describe more precisely the configuration that does not work?
What is the model number of the D-Link hub?
Which port is the hub plugged into?
Have you tried both ports on the back panel?
Have you tried connecting the hub to one of the motherboard ports?
Have you tried connecting the hub to the keyboard port (the upper port), connecting the keyboard to the hub so that it is there when power comes on, then turning the power off and on again?
The SAM has a "feature" that works like this: If you try to interrupt the boot sequence with the keyboard (to get into U-Boot), it only works the first time you switch the machine on. If you reset the machine (without turning off the power) and try to interrupt the boot sequence again, it won't work. You have to cycle the power to make it work again. Are you sure you are not being tricked by this?
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