i needed to do this and I think I ran into permission problems as well.
the solution I resorted to was , uploading the file to a temp folder in the same domain, /uploadtemp ( whatever ).
I set up ftp access to the folder i needed , in the call back function of the uploader, called a php page to ftp the files to the other server, then unlinking the file in the /uploadtemp dir.
might be a bit of a round about way , but the user is unaware of whats actually happening anyway
hope that helps