Same here with GOG, never had any mods. Selective cleaning of "AppData\Local\Larian Studios" folder didn't help (didn't want to delete it, as I'm 10 hours into a new playthrough already). No issues with the game itself, just this pesky warning in the launcher.

Considering how many people are reporting it, it's got to be a false positive - wrong checksums rather than corrupted files, for example.