Hi Leon,
I guess "a restart of NetWeaver cluster services" is something different than "a complete restart of NetWeaver cluster". Then such errors are quite expected. It is possible that the system failed to send a successful response for SFC Complete due to XA issue that in turn tirggered alarm via JMS. Due to the same XA issue, the system failed to roll back the transaction - thus you see the SFC eventually completed successfully.
Regards,
Sergiy