http://www.winuae.net/files/b/winuae.zip should really fix it.
EDIT: "Problem" is hq2x which is special (compared to most other shaders), it needs both original screen in original resolution (so that it can match pixels correctly) and also output screen in final resolution. I had to add "middle" shader position which takes original resolution and outputs final resolution which is between pre and post shaders.
Most other shaders work if input and output resolutions are same.