Strange; it didn't make a difference when I tried (checking the 'latest' download link to see if there was an update, though, it is at 1.14.0, while the version I have is 1.14.1). If that wasn't something fixed in the .1 update, maybe after the first time you manually set it to the correct file type for a profile it will remember that for the next time regardless of the setting. Or there was a glitch the first time that caused the extracted save not to show up.
It shouldn't affect any other new regions in this playthrough, since there were no other level files in the save earlier than they should be.
It could theoretically affect future playthroughs, though in general it is fairly rare. Quitting the game and deleting the files in the '..\Documents\Larian Studios\Divinity Original Sin Enhanced Edition\LevelCache' folder before starting a new game should make sure it doesn't happen again.
