How to prevent Steam to automatically validate files?

Do you mean updates? You can't stop them, short of staying in offline mode forever.

i'm pretty sure i saw a "no autoupdate" option for each game. meaning its in the preferences somewhere, and if you have a lot of games, it might take you a while.
but i may be wrong. sorry couldn't help more

I'd try reinstalling steam. And scan your hard drive for errors. If it's validating steam must think something is corrupt/missing.

I have this issue with a mod at Skyrim. I had to make the file(s) readonly so steam wouldn't overwrite it. Of course this also means the game cant modify it either.

I doubt it stops the verification process though.

-edit- : your issue would indicate Steam has an outdated version of the game(maybe let them know)? (unless your harddrive is failing)

-edit2-: are these files compressed by Windows, if so, that might be it?

Try running Steam in admin mode.
If the doesent work, try disabling auto startup. And run it manually.