Here's a short article on security clearances for those who are unfamiliar with them. If you're headed to En Route, you're required to receive a Secret clearance. Terminal positions are a Position of Public Trust, which is less involved and typically goes through much faster.
Clearances can take a while to go through. My own observation's been that they seem to go faster for ATC than for private companies. Maybe they get moved up the queue since it's considered a more pressing need?
If you'd like to read more, there's a pretty good (and long) FAQ here, in PDF form: http://www.clearancejobs.com/security_clearance_faq.pdf