So when you're trying to find the problem with an FME workspace, the key part is finding *where* the issue occurs. Here we want to know if the reader is failing to produce valid data, or the reader produces valid data but the writer fails to write it.
So, can you open the FME Data Inspector tool and in there open the PDF? Use the same parameter settings as in Workbench. That way you can see what is being produced. In this case it should be fairly straightforward: either it is producing a raster feature or it is not.
If it does produce rasters, then go back to Workbench and turn on feature caching using Run > Enable Feature Caching. Then click on the PDF object on the canvas and on the buttons that pop-up, choose Run Just This (a tooltip will show which option that is).
You should get a green icon on the object once the workspace has run. Click on that to inspect what the reader is producing. If it's not producing raster as the Data Inspector did, then the parameters might be different. I would suggest re-adding the reader, this time making sure to use the non-spatial options as the reader is added (rather than just changing them later). Then try running the workspace again.
If it is producing raster, then the GeoTIFF writer would seem to be at fault, although I really can't imagine what the issue would be.
Anyway, I've managed to get this working, so I think it is possible. So keep trying and - as RedGeographics suggested - if you can share one of the PDF files, it would really help.