i am not in front of my audya just now but think you do it this way:
pop your usb drive in one of the front slots. (probably be best to have folders on there already: single, block, midi etc)
go to 'disk'
then navigate to the desired folder so you can see your files using the cursor/enter keys.
press disk menu.
highlight all the files you want to copy by using the cursor keys and pressing the enter key to put a little blue dot by them (can be as many as you wish)
select copy (or move) using the F keys
select your target destination (D:remov) followed by the folder you wish to place the files in.
then I think you have to press execute (one of the user keys maybe 5/10) and then confirm
and thats about it.
On another note, have you tried the Audya on another computer? We have never had a faulty USB port here in the UK, but we did have one customer who had a problem when connecting to a computer. It turned out to be an issue with the USB driver for his USB port not the Audya that was causing some devices not to register. His printer worked but when he tried a Nikon camera that would not work either.
[This message has been edited by Tonewheeldude (edited 10-15-2010).]