Hi @carstengroen
"However, when selecting between the 48 and 96 MHz FRO I see that the FROCTRL trim values changes, so I guess that both FRO's are indeed factory trimmed. Can you confirm this ?"
Yes, you are right.
The FRO (12/48/96 MHz) of LPC546xx is factory calibrated (± 1%).
You can refer to these chapters.


"Why you can still measure −4% on some boards?"
Even if the factory has been adjusted by ± 1%,
Environmental factors, especially encapsulation, can still cause significant additional deviations in internal RC/ring oscillators.
Hope this will help you.
BR
Harry