If you have HDD's conflicting during startup it's probably because two or more of them have had operating systems installed on them at some point. This can lead to there being more than one master boot record which can in some cases, on some systems, confuse the heck out of it. Even if you have formatted an old OS partition, the master boot record may be a separate partition on the same drive and may not have been removed.
This is why when you relegate an operating system drive to a backup or storage drive, you should first use windows built in or a third party partitioning program to remove ALL existing partitions on the drive, then create a brand new partition on the drive and format it with the desired file allocation table (ie, fat32, NTFS, etc.) so there will be no remaining boot record or partition on the drive.
There could be other reasons for conflicts, but that would usually only be on much older systems. A faulty motherboard could be causing issues as well.
What are your system specs?