I was able to get this working. The problem that I ran into from my previous post was that I was still trying to run the service that I created using NSSM as the “Local System Account”. As a result, owncloud did not have any configuration to use and thus would not run.

Setup:

1. Whether you are on a local system or a file server in a Active Directory forest or Windows domain setup is create a dedicated user in the domain or on your local accounts. This probably should be a standard user for security purposes.

2. Log into the target computer that you want to run ownCloud as a service. This will create a User profile on that computer.

3. If you have not already installed ownCloud client, do so now, and then configure it while logged into the target computer with the dedicated account. Test the sync – make sure everything is working.

4. Log out of the target computer and log in as an admin user.
Download NSSM: http://nssm.cc/download/?page=download
There is no installation necessary, please follow instructions on their site for proper usage.

5. Install the owncloud application as a service. The command I used was (your mileage may vary):
C:\nssm-2.16\win64\nssm.exe install ownCloud

It will display a dialog box, enter the following:
Application: C:\Program Files (x86)\ownCloud\owncloud.exe
Options: (blank)
Service name: ownCloud
CLICK THE “Install Service” button.
You should get the message: “Service “ownCloud” installed successfully!”

6. Go to Services (services.msc)
Locate the ownCloud service and double-click it.

Service Configuration:
General Tab, Startup Type: “Automatic (Delayed Start)” This ensures that the networking
and other system components are fully available before attempting to start ownCloud.
Stop the service (if it is running).

Log On Tab, tic the “This account:” radio button. Fill in your user account credentials. If you are using a domain or AD account, make sure to enter the domain name and username “domain\user” format.
Click Apply, it should test credentials and let you know if you entered everything right.

7. Go back to the General Tab, and start the service.

NOTE: OwnCloud will now be running as a service and should sync normally. There is NO GUI, so you can not see the status and there is no indication it is working other than the service starting with no errors. If you ever need to update or change settings, you should stop the service, login in as your dedicated owncloud service account and make the changes in the OwnCloud configuration. Then close ownCloud and start the service again.