I think I remember what the error was..
it was a hack interfering.. I think it was vboptimize..
It had a setting, telling
vb to group javascript and put it at the bottom of page.
but the flash uploader is generated by javascript.. and thus it is sent to the bottom.
disable those options in vboptimize and it should be back on the top.
Luc
If i remember correctly it also said that this setting will not work on all pages.