Did you update your windows recently? There has been complaints that it makes it slow to boot up some people have to wait hours before it even boots, seems like a conflict between windows and anti virus programs.
I deselected the best answer selection, not sure why that reply was picked.
You need to go over your setup and check what programs are running, run an anti-virus scan. Best thing just start with a clean Windows setup and see how that runs. If you have issues with either of your drives that would cause slow boot, you can run the disk vendor check utility to see if there are any issues with it.