GOG support sent me this email when I placed a trouble call about FTL not running from the galaxy launch button, but being able to launch from the desktop shortcut:
May 15, 14:25 CEST
1) Please make sure that you use "Run as Administrator" to install and to start the game (right-click on the shortcut or setup file and select "Run as Administrator"). If you are using Galaxy, then make sure to run Galaxy as Administrator.
2) Please reinstall the game AND add it to your anti-virus/firewall software's exception/trusted list. Simply disabling firewall or AV software could not be enough, since some of these software are running still in background or in services list. If you are using Galaxy, then please add Galaxy as well.
3) This game supports cloud saves.
If you have the latest version of Galaxy(1.2.6) then could you please disable cloud saves and see if the game launches?
In order to do that, please:
- Launch GOG Galaxy.
- Click on GOG.com logo in the top-left corner.
- Select settings - > Features.
- Uncheck cloud saves.
None of these things worked for me, however. Mayhaps they shall work for thee? Who knows. But I feel it's a galaxy thing, not a user/client thing.