Atta's 2 roommates from Hamburg, also 9/11 terrorists, entered the US on January 15, 2000 (Los Angelos) after attending a meeting with Kalid Shiek Muhammad in Kuala Lampour.
This is from the 9/11 Commission and was reported long before the Commission started its work.
No doubt, DOD was looking for KSM at the time and it wouldn't have been hard to connect the dots to Atta from this information if you had access to it and were actually looking for terrorists (unlike the FBI and the Clintons.)