When 'WYSIWYG image filtering' option is turned on it preserves what you see when you apply the effects with Comic Life - in other words, it is What You See Is What You Get when you export your comic.
It keeps your filtered images at a 72 dpi regardless of your export settings that you have applied. This is why at the larger dpi export settings your normal photos will look fine, but the photos with filters will look pixelated. Remove the tick if you do not want the pixelation.
Please note: removing the tick will cause the filter to look less pronounced.