In retrospect, one of the major things that came out of 9/11 was a focus on terrorism - which meant we weren't paying much attention to whatever was going on in the ex-USSR as it slid into, essentially gangster control. Meanwhile, Putin was using 'fighting terrorism' as a reason to re-invade Chechnya, staging some terror attacks, becoming perceived as a 'strong man'. The neo-cons in the administration couldn't say much as the US was invading Iraq on similarly flimsy grounds. And I suspect the Russians reminded them that they were a nuclear power (the saber rattling we're starting to expect from them of late).
Just my $0.02, of course...