I hear ya, I downloaded the iexplorer for the computer, and using it I can see my iPad files, but it will not let me drop the goodies into the doc folder.
I think I remember having a problem dragging and dropping. I noticed if I tried to drag the rom by clicking on the name of the rom and dragging it, it would not work, but if I clicked on the folder icon next to the name and dragged, it would work. Did you try copy and paste?