Never had any problem with WinUAE. I'm 110% sure you've messed up while configuring.
Ah, in case you've got a Radeon you've probably got the Catalyst set to "centered timing" instead of "keep aspect ratio". If it's on centered timing it won't stretch the image to fit the screen, it will place the unstretched image in the center of the display.
Here's settings that give me a normal fullscreen image:
Ph'nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn!
"The sky was the color of a TV tuned to a dead station" - Neuromancer
ill check radeons settings.
