What is on the IDE drive? If any of the start up programs are on the IDE drive, it could be a matter of complication in retrieving them. I would also look into setting the IDE drive to slave instead. Could be a situation of conflicting authorities.
The IDE drive has some data files on it and an old installation of Windows XP, nothing from the Win 8 installation should be there as I installed it on the SATA drive.
As I said in my original post when I unplug the IDE drive the system loads up fast without issue.
I did originally have the IDE drive set as Slave but it wasn't working so I set it to Master, for one or two boots it booted fine and then went back to booting slow.