Steam – What games save to the Steam Cloud

Yes, you can trust it. It is non-intrusive and all it does (at minimum) is manage your games and patches for you. Anything else is optional.

Steam has an offline mode, where you can play your games without a connection to Steam, granting you total freedom from Valve's servers.

It doesn't install anything but the software you need (like DirectX and drivers for example) and the games and patches. Nothing you don't want, unless you don't want the game you're installing. The only downside is that these patches are kind of forced on you, even for single-player games. If the developer decides to 'downgrade' the game or make a change you don't like, there's not much you can do about it.

I'm not aware of any 'independent verification', but the DRM Steam is itself is very harmless, you can choose to run Steam in offline mode and there would be absolutely no way for them to pull access to your game, except for the fact you wouldn't get patches. Any other DRM can be chosen to be used by the game itself of course, but that has nothing to do with Steam.

Anyway, the choice to use Steam has already been made by Square Enix. If you don't trust them, why are you installing the game itself?

I know of only one way that this can happen in windows, and has nothing to do with Steam other than their not-so-great decision to install all content into Program Files.

If you are on Windows 7 or Windows Vista, and you have UAC set to ON, then change it later to OFF, this can happen.

UAC does thing evil thing where if a program tries to write to a "protected" area like Program Files, EVEN IF YOU ARE ADMINISTRATOR, when you get a UAC prompt and give permission, it actually writes any files that would normally go into that directory into a "virtualized" directory somewhere else.

If you turn off UAC, that will no longer happen, and as an awesome bonus, it will no longer know about the files that it virtualized.

So in your case, if you had UAC on, installed a ton of games, then later got sick of UAC and turned it off, this would happen as you described.

See the second paragraph in "Features" in the article on User Account Control.

If you have done this and turn on UAC again, your content will come back, but be a TOTAL mess because if you've downloaded more stuff with UAC off, then that will be invisible when you turn UAC on, and vice versa.

this drove me a little crazy once before I realized what was happening.

i'm curious to know if this is your issue.