I don't know if this is the same thing that happend to me. But when I first got my Mk2 I tried running empload on two different windows machines over the serial port. As soon as I got home I use USB and it worked fine. Then the next day I tried serial again on the same computers and it worked. So to me it seem like there was some inital state that would not allow regular serial to work, but after a sync with USB then it worked. It was back in the days of beta11d and I reported it to empeg but didn't know what it could have been.

-Finally received my Mark2 no thanks to customs.