I know it doesn't solve your problem, but I can verify that what you describe with icons being different sizes does not occur on any Win7 install I have used. For me, I can resize the icons with the CTRL+scroll method and any additional icons I place on the desktop are the same size as all the others.

On a more helpful note, for organizing desktop icons, I've become a fan of Fences. It lets you organize and hide your icons in "fences" on your desktop. You can even stuff more icons in a fence than it has area to hold and will be given a scroll bar to view them all. Might be worth a look.