I've been noticing some problems with pdfs, too. All I'm trying to do is read the darn things - not even annotate yet. Google books pdfs with images don't work well with Adobe for eReaders from what I can see. If you want the original formatting, typeset, etc - you need the pdf not epub version - but the Adobe software is only showing the text and blank spaces where the image should be and zoom doesn't work. It's fine on the pc. Books scanned by Microsoft seem to be just fine, text and images showing up together and zoom works. I've had issues with some pdfs only displaying the full title and author in the upper margin of the eReader side but the actual pages are blank. Haven't tried those on the pc yet to see of Adobe for the pc works, but I suspect it does. I'd like Adobe to make the eReader more robust like the pc version. I've written Adobe about this issue, but never heard back.

For now, I open each file on the eDGe to see if it works. If it doesn't, I delete it since I don't know when or if there will be a fix to this. I believe enTourage is trying to work around Adobe to get a greater variety of pdfs to work with the eDGe, but I don't know how successful they will be. And, who knows if Adobe will make the changes to their software?

Oh, as a humorous note, I've tried some color pdfs on the Docs to Go pdf reader and some work great! But others look like a watercolor painting that someone has thrown a bucket of water onto. Running color down the pages. I'm writing Dataviz about it. But, it does look quite funny ;-) Oh, Docs to Go doesn't even open the Google pdfs with illustrations or other problem pdfs. They just have big red Xs through the pages. So, the running colors show up great in B&W on the eReader side.
And, like you guys, all of these files are public domain so there shouldn't be a DRM issue at all.