Andrew, thanks for reporting this problem. This sounds a little like https://trac.transmissionbt.com/ticket/5246#comment:9, which was fixed in 2.77. Could you try upgrading from https://launchpad.net/~transmissionbt/+archive/ppa/ and see if this resolves the problem?
** Bug watch added: Transmission Trac #5246 https://trac.transmissionbt.com/ticket/5246 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1130442 Title: Starting a new torrent saves files in folder of previous torrent. To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/transmission/+bug/1130442/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs