I'm on OSX Snow Leopard (I had the same issue on Leopard, though..) This is the applescript:
tell application "Finder" to set my_from to selection
tell application "Finder" to set my_to to target of window 2
tell application "System Events" to keystroke (ASCII character 31)
tell application "Finder" to move my_from to my_to
It moves the current selection to the second Finder window, but before actually moving it advances to the next file by pressing arrow down (I'm in list view), so that I don't lose my position everytime I move something.
Problem is: it works every other time! You actually have to execute it twice to make it work!!
Anyone has an idea?