This is likely to solve the problem:
1) Right click on the new window name on the task bar
2) Click on 'move'
3) Press the down arrow key
4) Move mouse so that window is where you want it to be
5) Click when you're happy with #4
If it doesn't, I vaguely remember a setting somewhere in PT that allows you to reset window positions. More help may also be available at
www.pokertracker.com