Hi Peet,
Running as a service is more robust approach (watchdog of failed services). Other than that I can't see a real difference execution wise.
I still think running as a service is working and it is all about proper configuration. We had a support case lately with your same exact phenomena and the solution was configuration settings changes only as I stated above (make sure the service is running under SYSTEM and MDRV under IUSR_METRO).
If it dosen't work or satisfy your needs I guess a support call is your next option.
Happy to assist.
Thanks,