Partitioned Hard Drive issue

I installed a second hard drive, formatted it, partioned it into 2.

Then I decided to shrink my origial drive which was already had 2 partitions.

I shut down and it rebooted just fine.
But now I noticed these folders in the new E: partition:

Boot
bootmgr
BOOTSECT.BAK

I know these files were previously on my C: drive, but they are know gone, placed on the E: drive

In Disk manager my C: drive is listed as (Healthy, Boot, Page File, Crash Drump and Primary Partition
My D: drive is listed as (Healthy, Proimary Partition
My newlly created E: drive is listed as (System, Active, Primary Partition)

Is Windows picking up these boot files on the E: drive on startup for some reason?
I tried copying the Boot directory to the C: drive, but it would not copy two files which said they were being used by the OS.

I also noticed the E: drive was the first partition on the main hard drive, C: was listed second, and D: was listed last.

What options do you think I have?

I have no problem doing a re-install

Thanks for any help you can give

Generally, the BIOS chooses which is HD0, HD1, HD2, etc. for each of the hard drives on your system. The primary partition on the lowest number hard drive (or the hard drive that is booted) will be drive C.

Most people partition hard drives with either:
1) One primary partition, then an extended partition with logical drives in the extended partition.
2) An extended partition with logical drives in the extended partition.

If you have 2 hard drives with primary and extended/logical partitions. the primary partition on the first hard drive is drive C, the primary partition on the second hard drive is drive D, then the extended/logical partitions follow.

The preferred setup is to partition the first hard drive with a primary partition, then add extended/logical partitions if desired. The second hard drive should be set up only with extended/logical partitions. This prevents drive letters being changed if you remove the second hard drive.

Another option which I use is to have a primary partition on each hard drive, but I choose which hard drive to boot using the BIOS boot menu (I can press F12 at the first splash screen to get the choice which drive to boot). This BIOS boot menu option is probably limited to only some PC's. I have a ThinkPad with this option. When I do this, the drive that is booted becomes the C drive, and the second hard drive the D drive (extended/logical partitions follow).

I've checked the BIOS and boot options and they show the C: drive as the boot partition

So you're saying I can delete the E: partition and should not have any boot problems.

It's been quite a while since I've used fdisk beacause you can perform those operations though Disk Management.

I realy don't recal what the options were when i right-clicked on the drive. I always choose Simple Volume, I don't rememberr if logical, or extened being an option. If I remeber correctly in earlier version of Windows, you could create 4 partition, either Primary or extended and extended partition if you wanted to create more than 4 partitions on one hard drive.

It still bothers me that the E: drive is listed as a System drive and the fact that the Boot and bootmgr directories are not on the C: drive and the other file bootsec.bak is not located thetre either.

I'm not exactly sure what happened in your case without looking at it myself. FWIW, the newer versions of Windows can be installed on a Logical drive in an Extended Partition. They do not require to be installed on a Primary Partition. AFAIK, you do need a primary bootable partition for the boot loader (MBR), but this can be quite small. As examples: the boot loader can be GRUB, System Commander, OS/2 boot manager, or Windows.

I read: by default Windows 7 creates two partitions on install, unlike previous versions of Windows.

How to Avoid 200MB Hidden System Partition From Been Created During Windows 7 Installation » My Digital Life

Sorry for the delayed response.

I ended up reformatting.

Regarding the 200 MB partition, that doesn't apply, because I always format the drive before install.

I always wondered why people stated they had a 200GB partition, know I know why.

Thanks