This is something I've got going on with another person on campus. There were a number of issues among this. The user has a folder of all her office documents, and when she double-clicks to open one, it will come up in the appropriate app (Word and Excel are the two most used), and after a few seconds (after it is completely opened and all the pages have been counted or what-not), it switches back to the window from which she opened the file.
It is a Windows NT 4 machine running Office 2000. It is not limited to just her account, I tried a couple others. Applying a fresh image to the machine fixed all her other problems, and seemed to fix this one, but it came back as I was having her try it out.
My idea is that it has something to do with her own roaming file, and then it somehow spreads to the local All Users profile.
Any ideas?