So i recently began getting message "GOG Galaxy cannot launch because it is already running on another account on this computer." on startup (i think it coincided with updating to new Windows 10 Fall's Creator Update, but i am not fully sure). And it happens again even after fresh reinstall of Windows 10 (the newest build). This message pops, but Galaxy still launches soon after. So i unchecked "Launch GOG Galaxy at System Startup", and yes - after restarting GOG Galaxy still launches on startup, yet it isn't in Task Manager's Startup tab anymore and there is no shortcut in
C:\Users\<YOURUSERNAME>\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup folder.
I also can't find it in a registry (HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run).

So why does it launch twice? And where is this trigger that cause the additional launch?

You should check HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurentVersion\Run. The HKEY_CURRENT_USER is just your specific profile, while the HKEY_LOCAL_MACHINE is your entire system and most run at start items will be found there.

To add to what cogadh said, there's also the C:\ProgramData\Microsoft\Windows\Start Menu\Programs\StartUp folder for all users startup folder (from what I recall). But the Startup tab in Task Manager should be listing all said instances, no matter where they come from.

Thank you guys, but unfortunately there is nothing related to Galaxy in any of these two places either.
I reinstalled Galaxy, and after the first restart everything was good, no error, but after second time the problem repeated again...
That is indeed the weird thing that it launches when there is nothing in Task Manager related to Galaxy (when i uncheck that option in Galaxy itself).

Its the same problem (or feature) as described here:
answers.microsoft.com/en-us/insider/forum/insider_wintp-insider_desktop/programs-autostart-after-boot-in-windo ws-10/09dd8d3e-7b36-45d1-9181-6587dd5d53ab

Try using the old commands "shutdown /s /t 0" (shutdown) or "shutdown /r /t 0" (restart).

Maybe GOG Galaxy can make better use of the RegisterApplicationRestart API, see here:
howtogeek.com/275739/what-is-the-difference-between-shutdown-r-and-shutdown-g-in-windows/

That actually makes sense, thank you. So i suppose more people are going to face this "feature" once they upgrade to the newest build.