I'm really sorry about that @tim. We are at the mercy of Adobe's image exporter here, unfortunately.
That's one of the many reasons that we have been doing everything we can to move away from Adobe Flash/Air, and move towards a native application. PDFs in that application will be full resolution SVGs, rather than compressed BMPs. We should have more news about that soon!
If you're able, I would highly recommend that you update your copy of Mockups 3. We have added a lot of great things to make wireframing even easier, as well as implementing a backup system just in case something happens to your file.
We are working hard to make high-res PDFs a reality, friends. We will talk more soon!