windows on separate hard drives conflicting?

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Guest

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I have 2 hard drives, a PATA and a SATA, both plugged into the same PC. Recently i ran into a Castrotrophic disk failure due to my bro applying his wits, taking all my precious college research away. I decided i will install 2 copies of windows on 2 hard drives, one for my bro and one for me. I installed win 8.1 on both drives but soon i realized that when i ran one drive, then ran the other, there was some or the other problem in drive 2, usually all related to file system being corrupt and unreadable. The same happened the other way. Also, both hard drives detect each other and windows shows the other drive as a local disk. Please help me.
EDIT
This is the 6th time i am refreshing or resetting windows and none of them has a jumper installed making it primary or secondary
 
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No i am not, rather i choose to select the preferred drive from the boot menu, but the sata being the primary in the boot order.
 
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Guest

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Thanks a lot you are a great help. I will update the thread as soon i get that up and working . cheers :) BTW is it normal that the other drive shows as local disk
 
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shag00

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Dec 29, 2010
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Yes, the other windows installation will not look like a windows installation although the file structure will obviously be the same and yes the other disk will show show up as drive D:
 
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