I am having a real hard time duplicating this on 1.4, it just seems to happen from time to time in FF. When you click the upload a file button in a thread, the upload dialogue box appears under the browser. I have to minimize the browser window to see the upload box. In fact, it just happened while posting this thread here. Many times closing the browser and restarting fixes it. I thought it was just me, but some of my other users are reporting it now too.
So far, I can only confirm this happening with the flash uploader in Firefox. I haven't seen it happen in Chrome.