The function setFileFilters() is internal to the plupload javascript, and is called only by itself, so the only theories I have are a corrupted plupload.full.js file or a bug in it. Since I can't find any references to anyone else having this issue (on the plupload forums), perhaps it is a corrupted file? Try getting a fresh copy from the GSP download and replacing your file with it.
Roger Martin
Creator and Lead Developer of Gallery Server Pro