I've spent a couple days trying track this down,and finally found the problem.
In my situation, I upgraded a vs2005 project to vs2008. Once in vs2008, I decided to add ajax functionality. Whenever I would use the ajax uploader, it would do a full page reload after the ajax button click upload. Even the simple-uploader was doing it. I then tried to do a basic button on a page and the same results. After significant investigation, I found that when I converted from vs2005 to vs2008, there is a web.config setting that was causing the problem.
<xhtmlConformance mode="Legacy"></xhtmlConformance>
Removing the above line (or changing it to transitional) fixed my problem.
Just wanted to report this here, in case any other ajax upload users encounter this problem. Hopefully you can find it in the search.