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The old U-Boot (the stock one) contains old version of ARM Trusted Firmware (ATF), which has wrong initialization of USB3 PHY. This was not problem for old kernel which did not use ATF's code for phy initialization, but became a problem for new kernel. Check whether we run with stock U-Boot, and if yes, remove USB3 PHY properties from the device tree. The old U-Boot initializes USB3 PHY on it's own.
