Not doing a "clean" install, often leaves the boot partition from the previous install there. You can reinstall until the cows come home, but if there are multiple boot record, whether it's an MBR or a GPT, it can cause the system to go all skitzo. You have to choose the "custom" option during the install, delete ALL partitions on the drive, create ONE partition on the drive using all the unallocated space and then pick that partition for the install.
You also have to make sure there are no remaining boot records on OTHER drives attached to the system that might still be there but are hidden. You can attach the drives to another system and run disk management to see if there are other partitions aside from the main one, that might be causing a boot conflict.
Looking at the image below, you'll see the top partition is Windows. The bottom two drives have one partition each, with no partitions that do not have drive letters, or system partitions or unallocated space. That's what you want to see on storage drives, unless of course you intentionally have multiple partitions on that drive to separate the drive for organization or another reason like a restore or backup image of the OS.
On the image below you'll see what could potentially be a problem during the boot process. The image shows the top drive with the windows 7 OS installed on it's own partition and it also has a system reserved partition, which is ok and depends on whether the installation was done in legacy with a master boot record or in UEFI (AHCI) with a GPT partition like windows 8. In some cases, like the above image, you'll see the OS drive has no extra partition at all. The area circled in red below is the boot record for the drive and has a drive letter.
The drive below that, with Windows 8 installed could be considered like any storage drive where the OS and partitions were never removed. See the section circled with green that has NO drive letter. That's also a boot partition. The drive below that has unallocated space, which is abnormal and likely a result of a partition that was deleted but never rejoined with any of the other partitions to make use of the space. The area at the other end of the drive that is 200MB and says EFI (System partition) is likely ANOTHER boot record. So this system has three drives, all with boot partitions.
This can have different results. On some systems, depending on what OS is installed and how the BIOS is set up, it might boot but have a long pause, might boot normally or may not boot at all because with three boot partitions it's possible for the boot manager to become confused as to which partition actually contains the correct boot record for the OS installed on the C drive. Most of the time it will go directly off the boot record most relevant to the OS but in some cases, especially if they are similar records both pertaining to the same OS version, it may not know which one to use and could pick the wrong one or take a long time determining which is correct.
Therefore, any secondary disks showing partitions like this from old installations should be removed from the drive or the entire drive should be repartitioned so all of the available space on the drive is being used and no irrelevant records remain as partitions.
(You can click the arrows over here to the right at the bottom of the image to expand it for easier viewing----->>>>>^^^^^
Partitions without drive letters will not show up in windows explorer or my computer, or many other utilities, which is why you need to use windows disk management or another partition manager to deal with them.
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