Slow bootup

I have a Win2K server at a customer site that after rebooting, seemed to hang on “Applying Security Policies”. The numlock light would still toggle, and the HD light was flickering, so I decided to leave it alone and let it do it’s thing. About 45 min later, it finally came up! It DOES have a set of mirrored drives (80 GB) and I thought maybe it might be rebuilding the mirror or something, but I never had this happen before. On the next reboot it came up normally. Anyone have an explanation for this?