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The beagle is the center the controlboard acts as a extention to the beagle , and I had it one time that the beagle did not see the cubes , replacing it worked.
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I put the new BBB in and flashed to RC6 and then 1.06s. Still same issues. I can do anything in the GUI, but it won't see the cubes. I've been slumming around today and picked up a BBB & controller from a Mercury for the price of a BBB. So when that arrives, at least it will for sure tell me if it's a controller issue. I'm betting you were right Tolip_wen. Somehow the FPGA has been corrupted and I can't seem to get it to reflash.
PS: It does look like the latest revision of the BBB does work with the controller (not 100% sure yet though) since it can run the gui.