It seems that auto reset is not working properly.
Try this:
Have you tried this
Device Manager -> Com Ports -> USB Serial Port -> Port Settings -> Advanced button -> Set RTS On Close
I've tried to sprinkle this info around my site but apparently need it in a few more places.
Paul Badger
from http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1202521165