i have the same problem with the firewall thing. only i upload just fine, i just get the warning from the tracker saying it can't connect properly. i don't get it either.
as for the other problem, have you tried doing it in the directory before the one where the files are.
like say the show you're trying to seed is located at
C:\ > Live > mmj2005-06-21.flac16
instead of selecting the mmj2005-06-21.flac16 directory select the "Live" directory and then when it goes to make the folder, it'll already see that its there and then check the data and start seeding.