Problem's now fixed in build 674 - binaries are at http://hypnosis.kicks-ass.net/testing
It originally did this to keep the window visible after resolution changes, but was not really done properly.
After every mouse click the main window re-centers in
the display window. Not only does this prevent a user
from placing it where they want (and having it STAY
there) but is a serious misfeature when the user has
an even number of displays (monitors). On my 2
monitor setup, it keeps placing the window across both
monitors making it VERY hard to read.