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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.