FreeHEP VectorGraphics, the library yEd uses for exporting to EPS and PDF, does not support EPS as well as PDF. Especially (semi-) transparent colors are not supported for EPS. Unfortunately, there is not much development going on for FreeHEP VectorGraphics. In short, export to PDF or SVG for best results.
It is not a good idea to post your eMail address in public forum like this one. For this reason, I removed your address from the original post.