My system originally did not show an associated drive with the Windows Boot Manager. It was only after a few Bios updates that feature showed up. My Z68 board is about two years old and has had several bios updates. But look at it logically. The system boots fine with just your SSD. The system boots fine with the second drive connected, if the errant space is not used. Your disk management shows erroneous information about all drives other than the SSD. One bad drive in a system can cause problems for the system. If you want to test, get another internal hard drive (remove the current one) and see if Disk Management shows it twice. If nothing else, you could transfer the data on your Logical partition to the new drive. Not really sure why that drive is showing a logical partition, but maybe you know. I also noticed that the bios default may be set to use IDE as the SATA controller type. Have you changed it to AHCI or is it still IDE? No reason to change anything, just wondering.