DC Shooter had "secret" security clearance

Excuse me, but there is something here I'm not understanding. We have been told ad nauseam that background checks will keep guns out of the hands of criminals but why will not background checks keep violent criminals out of government facilities? From Yahoo News;

Aaron Alexis, the 34-year-old suspect in Monday's shooting rampage at the Washington Navy Yard, had "secret" clearance and was assigned to start working there as a civilian contractor with a military-issued ID card, his firm's chief executive told Reuters.

Other sources have reported that Alexis had just returned from a month long visit to Thailand and that he had been busted out of the Navy after a series of misconduct issues. One assumes that discharge from the navy would have been less than honorable but in these days of heightened sensitivity toward malcontents the navy may have given him good paper just to get rid of him. Still, one takes an month long trip abroad where his activities cannot be documented and no one sees a security issue?
The issue here is not the availability of firearms but rather the availability of government access to men such as Aaron Alexis, Major Nidal Hasan, Private Bradley Manning, and Edward Snowden.