Without seeing your code, it's difficult to say what could be happening, but I'd guess the AJAX table update is rebuilding your entire table.
If that's the case, it'll probably override some values and listeners that the fileupload call set on them.
A solution would be to re-initilise the fileuploads after the AJAX callback, or to change the structure of the page, so your AJAX rebuild doesn't rebuild the elements controlled by the fileupload plugin.
Could you supply some code so we can see what's happening?
Cheers,
Stu