That just happened to me! I have been a contractor at a Fortune 50 company for a while and they opened a position for the job I'm doing. I applied and was rejected by the HR algorithm (the rejection email came about 2 minutes after I submitted my application so I seriously doubt that any humans were involved). The job site I had to apply through was taleo.net.
Centralized HR is for managing benefits and setting policies. They never help with the hiring process, in my experience.