Command line options
Are there any command-line options for this server? When I run this by a shortcut or by terminal, it doesn't load the .ini. But if I just click on the direct .exe, it will. I'm wondering if there is a command-line property to set where to load the config from manually as it starts, I'm trying to configure this as a windows service and it loads the .exe but it fails to load some of the servers (httpd, etc) & files with the executable.

Use FireDaemon.

My server isn't built to be a Windows NT service; you might be able to use Launch Service or something like that to load it like a service. You just need to make sure that it starts in the directory that contains its system folder.