Hahah, so I installed windows on the the hdd labeled Disk 1. Now in disk management the installation is listed as disk 0. Go figure. I guess there was never an issue. Why would windows label the disk 1 during installation and then show it as disk 0 in windows? Guess that is windows for ya Sorry for all the trouble.
There is no reason you can't have an OS on any disk you want. I only recommended putting it on DISK0 because otherwise during Startup Repairs or Reinstall the boot files can be derailed to the first Primary partition on the system. It's for this reason that I would either install Win7 to DISK0 or make sure any preceding partition to the disk it's on is Logical which cannot be marked Active to accept boot files.
Glad it sorted itself. How is performance?
You can get and keep a perfect install if you stick with the tools and methods in Clean Reinstall - Factory OEM Windows 7 which compiles everything that works best in tens of thousands of installs we've directly helped with here.
What I am about to say is not specifically related to the OP HDD's as he said they were identical but worth noting none the less, The BIOS views your drives differently than when your looking at them within windows itself there is a few reasons for this that are explained elsewhere on here, however if you have a slightly older BIOS and you have fitted a faster drive 7,500 rpm alongside a slower one it will not show up as being Drive 0 no matter how you set it up in the BIOS (or physical location) due to the older BIOS not recognising the higher transfer speed, it's not until you select to load drivers for said HDD that it will detect it correctly prior to a Windows install, problem being finding specific drivers that will work prior to an install... If not then don't worry about it many times even from within Windows I have seen the OS on Drive 1 until the Intel drivers are installed then just like in the case of the OP upon a reboot you will see Drive 1 is now Drive 0 and vice versa... Just a quirk in some cases with slightly older systems and more modern HDD's
Thanks everyone for your help. Thank you gregrocker for all your advice and the link to the clean install guide. performance is perfect so far. Nice to have a clean version of windows not full of bloatware and start-up crap bogging it down.
Marked as solved.
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