Users folders recreating themselves into duplicates

I recently switched from a Mac to a Windows PC and I have never had any experience dealing with multiple drives. I am currently using a 60GB SSD to boot from. I have a second hard drive named Storage. It's my D: drive. I did some searching when I purchased the computer on how to properly use a secondary drive for storage. I feel as if I didn't do it correctly. I moved my Users folders(My Documents, My Videos, My Pictures, etc.), not the Users folder itself, to my d: drive. Since I did so I have had odd things happening. It started when I renamed the Saved Games folder to Games and now my World of Warcraft icon on the start menu is now that generic application image. It will open up, the logo is just wrong. Also, I find that practically every time I start up my PC there is a new My Music folder identical to the original one (this sometimes happens with My Videos, too). It will often have a folder inside as well, today it was a folder labeled iPod with another folder inside it which was empty. The date created is always the current date and when I click properties>sharing the title of the folder is not actually My Music, but rather something like New folder(3). Any ideas why this is happening? I am stumped.

I'd like to bring this post back to attention. I am still having the issue and I'd very much like to fix. I am wondering if I should move all my users folders back into the Users folder and just create my own. Would that work? Here is a pic of my issue. The My Music folder currently hasn't recreated itself.

Okay, so right now I do not have a backup. Would it be okay to just create a restore point and then go about OPTION TWO? If so, should I place my files somewhere else outside of their current folders before I start OPTION TWO? Thanks.

Some work, some don't. I get this for the one's that haven't worked (all but My Documents, Downloads, and Desktop).

I got it to work! Thanks a lot, Brink. Any recommended articles for properly managing my files now?