We've run into this issue as well and have come up with a workaround until a real fix comes along.
On lines 69, 70, and 151 of the minified source, change all occurrences of "fileFilters" to "fileFilter".
On lines 69 and 151 change
"a.pluploader=new plupload.Uploader(… the parameters object ...) if (a.fileFilters!==null) a.pluploader.filters=a.fileFilters"
"var opts = … the parameters object …;if(a.fileFilter!==null)opts.filters=a.fileFilter;a.pluploader=new plupload.Uploader(opts);"
We've filed a support ticket for this as well. Hope you find this useful.
- HP w/ Couto Solutions