Hello, I am just trying to do the same thing in the LPC54114 board.
And in the <user manual> , it says: Effective processing of the externally supplied clock to the counter has some limitations. Since two successive rising edges of the APB bus clock are used to identify only one edge
on the CAP selected input, the frequency of the CAP input cannot exceed one half of the
APB bus clock. So perhaps you should try to improve your the frequency of your CPU (to 96MHz for example).
But I have encountered other problems: I have used the Burst Mode of DMA, which is triggered by Timer3. But it seems that when the frequency of Timer3 is greater than 3MHz, the DMA can not catch this speed.
Can you help me? Thank you.