Very strange problem. I found this thread looking to prevent Windows to assign folder templates automatically - I want all my folders to look the same. If I ever need a folder with photos to show thumbnails I can click the corresponding button, but otherwise I want the folder to look the same as all other folders. The registry hack shown in this thread seems to do the trick, but I will play with it for a few days to be sure.
Now, what is the problem with Explorer windows? If I close the Explorer and then reopen it - it shows up at the same place, it always has the same size, always opens to the same folder - naturally the one defined in the shortcut - and hopefully the registry hack will help me to get rid of the automatic template nonsense. OK, I can open more than one window - but surely if I use the same shortcut to do this they will keep showing up at the same place - you don't expect the same shortcut to remember how many windows you have opened? Or do you mean that you have more that one shortcut but they still don't remember their respective positions? Do you have them run as separate processes?