Top suspect is that it's being downsampled by your PDF JobOptions.
What resolution are you saving it at out of Photoshop?
As you probably are aware, when editing an embedded or referenced EPS (or PDF) in FM, what you see during edit is a thumbnail/preview image that is basically a GIF (72 dpi indexed color, possibly crudely dithered). You would also see that coarse image if you print directly from FM to a printer using a non-Postscript-like driver, such as HP-PCL. But what's sent to the Distiller stub on Print-to-PDF or Save--as-PDF is the full-res EPS.