Hello
Could you help us confirm that the "Update Code" option in Overview tab from Clocks Tools is enabled?
In [Functional group properties] in the toolbar, you can select BOARD_BootClockFROHF96M and enable the "Called by the default initialization function" so the BOARD_InitBootClocks initializes the BOARD_BootClockFROHF96M.

I notice in your first photo that when selecting the MAINCLKSELA it shows 48 MHz instead of the 96MHz; according to LPC5411x User manual [UM10914] Chapter 6 Table 153. FRO Control Register, bit 14 is fro_hf_output status bit, if read as 0, fro_hf is 48 MHz. If read as 1, fro_hf is 96 MHz.
Could you help us select in the clocks diagram the option FRO96 (fro_hf) and "Update Code".

Then in Registers tool search for SYSCON_FROCTRL>SEL to confirm its on 1 [96MHz]

Let me know your findings,
Best Regards, Luis