Hey there, RacerDemon!
It seems like you most probably had both HDDs connected to the motherboard when you were installing Windows on the primary drive. Unfortunately, having two drives plugged to the SATA ports at that time causes an OS confusion which makes Windows scatter the system files across all the HDDs. The best way to fix this issue is to start from scratch and reinstall Windows on the primary HDD with the secondary one UNPLUGGED from the mobo.
Once the OS is up and running on the booting HDD, reconnect the secondary drive and try reformatting it through Disk Management again. This time, it should work as long as your boot priority is properly configured in BIOS.
Clean installing/reformatting will erase all the data on those drives, so make sure you have backed up anything that is important from them elsewhere.
Hope this helps. Good luck!
SuperSoph_WD