Adobe Illustrator EPS to Adobe Distiller export problems

I'll generally work in an eps file format and drop those files into adobe distiller to get press ready pdfs, to keep my file size down. Anytime I have a photoshop file that has at transparency with an overlapping shape it'll clip the two when I drop them into distiller to export. (I'll leave an example below). Granted I know that PDFs really don't like transparencies, but I've never had a problem until two weeks ago. I can export a pdf directly out of illustrator and it'll look fine. 

Anyone else having these issues? I've tried several different ideas (saving to old formats, flattening things, etc.) to solve the problem but ultimately I really need a solution to get back on track.