Hi,
There is no issue running FCCU configuration from IRC clock.
Actually, FCCU is clocked by IRC clock (which is considered as safe clock).
I will explain your situation:
Once you unlock FCCU and move to configuration state, FCCU starts its internal configuration watchdog (not programable).
If this watchdog expires FCCU reports configuration timeout.
Also once you are in configuration state you can only work with FCCU registers (if you work with other peripherals you will get fault).
Write a simple example and replace with it the failing code:
1. unlock FCCU
2. move to config state
3. move to normal state
regards,
Peter