The designer of the inbuilt waitbar used a fixed absolute size for the bar's axes, defined in points. Apparently they did not consider that users might want to change the figure size and have the bar automaticallly adjust to suit... everything in that function is written assuming a fixed-size non-dockable figure.
You can easily change the bar's axes's units:
>> h = waitbar(0.5);
>> set(get(h,'children'),'units','normalized')
and then adjust the figure size afterwards:
>> set(h, 'Units', 'normalized', 'Position', [0.18,0.43,0.23,0.08])
As an alternative, it is not very difficult to write your own waitbar/progress bar: define a figure with axes containing a patch object, adjust the patch width.
You can also find plenty of waitbar submissions on FEX, some might have normalized axes too:
