Sorry, the edit period timed out and I didn't finish writing.
@seph oops fg-svc instead of svc-fg. That would be the problem. Yes, it isn't reading the config file because I was using fg-svc. I expect that will fix that problem now. I'll check on Saturday (it is weekend in this country now). The launcher.flag file is the same as on all the computers that I'm deploying with that MSI file, and the others are working.
This computer is one that is not reporting at all. I have another one I'm looking at now which was reporting but has stopped. This one gives me this log below when I run it in foreground using the correct command you reminded me of 🙂 I'm actually wondering if it might be having the same problem. In Services.msc this one shows that the service is running, it doesn't stop with an error, yet kolide server shows it is offline. If I then stop the service and use the svc-fg command I get the result below, even though I have confirmed that the launcher service is definitely stopped. So this time I took a backup of the C:\program files\kolide folder before uninstalling (In case you want it to check anything), deleting the kolide folder, and reinstalling it. However reinstalling it did not fix the problem.
"C:\Program Files\Kolide\Launcher-launcher\bin\launcher.exe" svc-fg -config "C:\Program Files\Kolide\Launcher-launcher\conf\launcher.flags"
ts=2019-05-16T08:38:59.2118496Z caller=svc_windows.go:58 severity=debug msg="foreground service start requested (debug mode)"
ts=2019-05-16T08:38:59.2178439Z caller=svc_windows.go:79 severity=debug msg="windows service starting"
ts=2019-05-16T08:38:59.225839Z caller=svc_windows.go:88 severity=info msg="runLauncher exited" err="open launcher db: open C:\\Program Files\\Kolide\\Launcher-launcher\\data\\launcher.db: Access is denied." stack="open C:\\Program Files\\Kolide\\Launcher-launcher\\data\\launcher.db: Access is denied.\nopen launcher db\nmain.runLauncher\n\t/Users/seph/go/src/github.com/kolide/launcher/cmd/launcher/launcher.go:227\nmain.(*winSvc).Execute.func1\n\t/Users/seph/go/src/github.com/kolide/launcher/cmd/launcher/svc_windows.go:86\nruntime.goexit\n\t/usr/local/Cellar/go/1.12.2/libexec/src/runtime/asm_amd64.s:1337"