[HKEY_LOCAL_MACHINE\SOFTWARE\Qbik Software\WinGate\Services\SMTP Server]
"Description"="SMTP Server"
"Startup"=dword:00000001
5.2.3 sometimes had an incorrect state for the startup of the service if you chose not to use the Email Server. The value of Startup=1 indicates that (Manual start/stop). A start/stop all of the services will only start non-disabled services. If you change the 1 to a 0 (I.e. Startup=0) then the service will be marked as disabled. This does require editing the registry, so ensure that you have appropriate backups, etc.
This will require a restart of WinGate to take effect, and you should make the modification after you've stopped the Engine.
http://forums.qbik.com/viewtopic.php?t=702&highlight=startup+smtp
That post gives a more detailed view of somebody also experiencing problems with the SMTP Server on an earlier version.