It's been a long time since I've done much with Windows and I don't have a machine to check myself, so I would be a poor choice to try and walk you through setting up a new Windows User account. Besides, it won't fix your current problems, or at least it's very unlikely it would. It was about keeping it from happening again.
I have no idea why your iTunes library would duplicate. iTunes can only point to one at a time. Without seeing what is going on, I can't even guess at anything else to try.
Regardless of what you do, your app purchases and iTunes credit are associated with your iTunes account, not your computer. Nothing you do to the computer will affect them (other than not letting you view them properly). To be certain that your important apps are still available for download, go to the the App Store on your iPad and check out the Purchased tab. Anything showing there can be downloaded again.
The same goes for any music, books, TV shows, or Movies you've purchased from Apple.
I have no idea why your iTunes library would duplicate. iTunes can only point to one at a time.
Give contacting iTunes Support a try. I don't know if they can help with this kind of problem, but it is worth a shot. The worst they can do is nothing. Or they could point you at Apple's iPad Support which will cost money if you are not on Applecare, but it's not like you have to go there.
Good luck, and I'm sorry I haven't been of more help.