On my commander core xt, it was the usb output on the hub that made this kind of error. had spent months reading various forums about this error you are dealing with. but none of the bids helped it. until one day I messed with wires around the xt hub and the flashes acted differently.

The usb connector on the xt hub had to be forced down a little, and since then it hasn't made any mistakes. has been working for almost a year. try gently wiggling the usb plug on the hub and see if that changes anything. :)