The only data (besides the files in the game's folder) the game uses is the registry branch, but it's only used to store in-game settings. You can try clearing it, but I don't think it's in any way relevant, it just stores the settings you can change from the game's UI.
Having some weird settings set for the game specifically in the video card settings would be a possibility if it only happened on the desktop machine with the nVidia card. The embedded Intel HD Graphics has pretty much zero useful settings, and those are certainly completely different from nVidia's.
I'm honestly out of ideas what it could be without looking at the issue myself.
If it's possible to install, say, a temporary clean Windows copy into another location just to test in a clean environment and see if the issue reproduces or not — that would be the way to exclude (or not) the software issues. Probably shouldn't mess with the VAIO's setup though if you don't know what you're doing, it can have a peculiar installation procedure, unless you can just stick in a spare drive for a test.