serbar, thanks for the feedback on this. i've been on vacation and haven't been able to dig into this too deeply. i skimmed the discussion in the link you posted.
in Fetch, have you tried going to Communication->Settings and trying each of the options for Handshake?
if none of those options work, we should be able to release something soon that enables DTR. we'll want to verify it doesn't screw anything up for other arduinos as well.