Windows are managed by the window manager. It controls the size and location of the windows appearing on the screen, trying to mediate between the slew of applications vying for the user's attention.
This means that even though the program can request a particular geometry (i.e. size and location), it is not guaranteed to get it; in particular, the window manager may decide to place the window somewhere else entirely.
HTK does not support all of Tk's commands to communicate with the window manager, but most of the important ones. These are the class functions of the Window class, as mentioned above, and the Screen.htmlScreen module, which allows you to query the properties of the display (e.g. height and width).