Right off the bat, the xlim and ylim were way off in the weeds (at least for the parameters i chose). Try these changes:
% use meaningful descriptions
x = input('enter x offset: ')
y = input('enter y offset: ')
w = input('enter width: ')
h = input('enter height: ')
% filter these once instead of a bunch of times
w=abs(w);
h=abs(h);
clf
% here, i'm adding [h/2 w/2] margin around the box
% that's just something arbitrary i picked
axes('NextPlot', 'add','XLim', [x-w/2 x+w+w/2], 'YLim', [y-h/2 y+h+h/2]);
% why are you using abs(x) and abs(y) everywhere?
% that makes the size wrong if x or y is negative
% if x and y must be non-negative, filter them first, like with w and h
for e = x:0.5:(x+w)
plot(e, y, '*k')
pause(0.05)
end
for e = y:0.5:(y+h)
plot(x,e, '*k')
pause(0.05)
end
for e = x:0.5:(x+w)
plot(e,y+h,'*k')
pause(0.05)
end
for e = y:0.5:(y+h)
plot(y+h,e, '*k')
pause(0.05)
end
