I am having the same problem as described in this post (http://forum.arduino.cc/index.php?topic=147645.0) but since it is old and not solved, I though I'd start a new topic.
I cannot see the serial monitor any more. When I open it it create a mini window in the task bar, but when I hover over the icon it just show a transparent window the size of the serial monitor.
I have updated Arduino to the later version, but the same keep happening.
Any ideas how to fix this? Many thanks