I think I have found a bug in system_LPC54628.c in the SystemCoreClockUpdate() function.
The observation is that when I run the core at 220MHz the SystemCoreClock variable ends up with 440,000,000. Measuring frequencies with a scope shows the clock to be correct at 220MHz. The knock on effect of this is that RTOS timers and scheduling run at the wrong speed.
I think the bug lies in these lines:
/* MDEC used for rate */
workRate = (uint64_t)clkRate * (uint64_t)findPllMMult(SYSCON->SYSPLLCTRL, SYSCON->SYSPLLMDEC);
clkRate = workRate / ((uint64_t)postdiv);
clkRate = workRate * 2; /* PLL CCO output is divided by 2 before to M-Divider */
I think the last line should read
clkRate = clkRate * 2; /* PLL CCO output is divided by 2 before to M-Divider */