We recently updated the version of Commons-Daemon that we use in TomEE. One knock on effect of this is that this now installs the service as the user 'NT Authority\Local Account' as opposed to 'LocalSystem'. Should this not be what you want, you can work around it by changing it either with the UI provided by TomEE.exe, or in the Service Control Manager.
Our batch scripts do take a "/user" property, but this simply controls what use the installation batch file runs as, not who the service logs on as.
A change is needed to these so its possible to specify a parameter to pass the service name and a means to capture the password.