Okay, I can duplicate the issue. It turns out that impulse isn't setting the permissions of C:\Program Files (x86)\Indie Games\AI War (and all subfolders) to be writeable for your local user account. This means that the save files and game settings, etc, are being stored in a really wrong place as well as the updater not being able to function (and the settings importer not working, too).
I've emailed Stardock about this, and hopefully it will be an easy fix, I think it was just an oversight on my part not mentioning that detail to them.
In the meantime, if you want a workaround you can manually grant yourself read/write access to that file path (the Indie Games\AI War folder) and all subfolders. You may then need to search your computer with the windows find feature to find your settings.dat file and save files (I have NO idea where it is putting them when it can't write to that folder, honestly -- would be curious to know, but I have too many copies of AI War installed on my PC to be able to tell very clearly), but then things should be working as expected.
Sorry about the confusion there, that's definitely an odd one!