Look at the Section 33.4.3.1.1 of the LS1046a Reference Manual. Do you use similar command sequence for USB 3.0 device initialization?
Look at attached file. It is LS1043a USB driver code from NXP SDK 2.0 Linux BSP. Similar code can be used on the LS1046a board.
See gatged.c file.
Have a great day,
Pavel Chubakov
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