Make sure you have the shadow_mask_alpha set to 0 and the scanline_alpha set to 1.0.
Also, try adjusting the scanline_size and scanline_height (aka scanline screen height and scanline individual height in the UI).
If you are using the default HLSL settings you may want to turn down/off the raster_bloom_scale. I think I have mine set to 0.1 for reference.
Also, I'm not sure why you are not using your monitors native resolution. Can you video card not handle 1280x1024? I'd think any card that can handle HLSL can do that resolution, but maybe not. Assuming the image is getting scaled to that resolution anyway, it's possible that what ever is doing the scaling is introducing artifacts that are affecting the look of the scanlines...?