If it's something like the CIA checking into him for possible corruption - that's a pretty thin charge to try and hang onto Stan, but then again they did bust Al Capone for tax evasion.

Maybe Proxy Snyder Agent Wolfe or his boss got tired of Stan's antics and started digging into the Nina thing. If so they might've realized there was more going on than in Stan's official reports, and decided to proceed with a way to charge him for treason; when they couldn't make that stick, they decided to liaison with the CIA to see if they could dig anything up outside of the country that could tie into Stan's possible charge.

I admit, it's pretty thin. :\