I've got a couple thoughts, but no real answer. My first thought is that you either have a flaky lnb or card, but I'm to new to this to say that with any certainty. I have a twinhan card and have played around with the various programs. I've heard that its best to scan without the disecq switch connected. In my case, I can't scan anything with the disecq switch in place. I'm not sure what to tell you about getting different polarities with and without the switch. The other thing you might do is try to scan with some of the other programs(progdvb, ritzdvb, etc). You might just have something messed up in your MT config.
Mike