If you run Config.exe in the game's installation directory, and click on Save Folder near the bottom, it'll open the directory where your save files are supposed to be. On my Win8.1 machine that's C:\Users\[MY ACCOUNT NAME]\Application Data\FALCOM\ED6 As far as I know it's unchanged since launch.

Edit: goglog.ini has a reference to C:\Users\admin\AppData\Roaming\..\..\Saved Games\FALCOM\ED6 On my machine this directory exists but is empty, and there's no equivalent under the non-admin account I use to play the game.

I seem to have a copy of the save directory under C:\Users\[MY ACCOUNT NAME]\AppData\Roaming\FALCOM\ED6 I'm unsure whether it's a distinct copy or just an alternative file system path, but you could have a look there.

Believe this will take you to the appropriate directory on XP, Vista, 7, 8, etc:

%APPDATA%\FALCOM\ED6

As VanishedOne mentioned, check if the saves are under the admin account or if you are running the game as admin instead of your normal user account. That's an alt system path; well actually the real one. The other is the alt path.

Thanks guys, I checked the second folder path and my saves were in that one. I moved them and was able to load them. Thank you for the help!

Tried uninstalling GoG Galaxy but no dice. I still am unable to save a game.
Fuck you idiot developers !