Herman,
I found that when the upload progress window is presented, the Contact Sheet window will lose focus. This is why the second FTP session failed for me, because there is no Contact Sheet document selected. If I click anywhere on the Contact Sheet to bring it back in focus, without changing the selection, I'm able to FTP to multiple destinations just fine.
If you bring the Contact Sheet into focus by clicking on it before your second FTP session, does it fix the problem for you?
-Jerry