This probably happens because you have set the frame parameters in the
initial-frame-alist. That variable holds parameters
used only for the first frame created when Emacs starts. To customize
the parameters of all frames, change the variable
These two variables exist because many users customize the initial frame in a special way. For example, you could determine the position and size of the initial frame, but would like to control the geometry of the other frames by individually positioning each one of them.