Hi Manuela,
There can be various reasons for external reset.
1. Yes, you will see F_SOFT_FUNC in FES register after writing 0x00005AF0 and 0x0000A50F in MCTL register.
2. External reset can be caused either by debugger or external event on external reset pin.
Disconnect your SBC chip reset line from micro to ensure reset is not coming from SBC.
I just made a test and I can see only F_SOFT_FUNC set in FES after writing to MCTL register.
Peter