When switching to multiple render targets before switching back to the back buffer, the saved viewport is set to the 2nd to last render target size. Basically, the code is assuming that the consuming application will set the render target to the back buffer before switching to another render target.
 
The issue is in GraphicsDevice.SetRenderTargetGL20. I suppose a possible solution would be to save the back buffers viewport size on initialization, and then just use that when resetting the view port when switching to the back buffer.