If you are not using the 32 Khz crystal, please set clk_cfg.useStandbyClk = CyFalse; and try,
In addition to this, you need to set the clk_cfg.clkSrc = CY_U3P_SYS_CLK;
Thank you, but this still doesn't explain why calling DeviceInit with NULL results in a 100.8 MHz GPIF clock. Is the documentation current and correct? If so, this should result in a 384 MHz system clock and 96 MHz GPIF clock.