From http://forums.atlassian.com/thread.jspa?messageID=257250330#257250330,

Disabling a build queue is not persistent between restarts. This is annoying as we have a number of build queues that all tried to run at once as soon as bamboo is restarted. I wanted to turn them on one at a time to make sure they worked. I ended up disabling each build individually which did work.

To replicate this scenario;
1) Create build queue
2) Disable build queue
3) Up on restart, the build queue's are enabled.

Thank you Mark(mg) for reporting this issue.