I had the Steam version originally installed (pre-order gift key) and then installed my TTG version. My (user)\My Documents\Telltale Games folder then had a GameData folder in it (with only the SyncFs folder and prefs.prop file in it) along with the The Walking Dead folder that contained my saves from the Steam version.
My TTG would not see the previous saves from Steam, even though it recognized I had the game installed, and I chose the "keepsaves and prefs" option during installation.
I disregarded (but not uninstalled) the Steam version and started a new game in TTG. Steam did not see saves from the TTG either, I checked after a save in TTG.
Later, I decided to uninstall the Steam version, preferring the TTG anyway.
I restarted TTG and my save game was not seen. Checked the My Docs folder and everything was as it had been.
I decided to start from scratch. Uninstalled everything and deleted all folders. Then reinstalled only the TTG version.
So far all is fine, and no extra GameData folder was placed in My Docs either.
I am wondering if the extra GameData folder had caused difficulties. I wish I had thought of it then, I might have tried just deleting the GameData folder to see what affect it had.
Anyway, just thought I would let you guys know about it :)