I understand that, please read update.

but how do i stop it from doing it?

First up, have you tried the suggestions posted by others?
Secondly, is Steam running in the background when you're launching the game? (ie. is Steam's icon in the activity field/whatever near the clock?) If so, try quitting Steam entirely (rather than just minimizing, which is what I think happens when you click the "close window" button).

No, same disk.

Are you launching it from the folder or a shortcut of some kind?

Really strange behaviour. The GOG version really shouldn't be making any calls that get Steam's attention.

Since the GOG version is built from the Steam version (it has "steamapi.dll"), it is is likely the Steam can detect when the game is launched (at least if Steam itself is running to begin with).

I figured it out, kind of stupid really. i forgot i changed the launcher with a modded one but i dont think it was working. i deleted the launcher and went back to the original. its all ok now

thanks for all the imput guys, i feel rather stupid making a fuss

Never played Saints Row 3, but maybe there is a community feature activated, something, like upload a video or pictures, which lets the game look for steam. Or something that is multiplayer related, something like team chat. Did you activate something in the game options that goes in that direction?

Normally steam should not start, because gog tries to remove anything that is dependent to steam. But maybe they overlooked something, and you unfortunately found and activated it. You can try to find that option by yourself, but you should really also contact gog support for help.

Other option: Backup your savegame and uninstall the game. By doing it hopefully all your settings are gone. Check maybe also others possible location for files, like my documents, documents & settings, AppDate, etc. Then reinstall it.

Edit: Forgot to ask, but is the gog version of Saints Row 3 your first one or was long time ago another one (steam, retail) installed and there are somewhere old settings and files in the system.

Edit: Oh, I was one minute too late to the party...

Great that it was solved, it is a nice game. Also, don't worry too much, everyone makes mistakes and this one was barely noticeable on the scale of mistakes.