I read almost nothing but PDFs on mine iliad, some very large (over 1,000 pages, over 100Mb). I've only had a problem with one 6 page article that was something to do with the way a figure had been created. There are limitations to the PDF viewer, most notably no built-in search. There are also community-enhanced versions that add additional features. Password protected PDFs can be read on the iliad, but not those with DRM.
If any of the PDFs you have had problems with on the cybook are freely available you could point us to them and we could check to see if they work ok on the iliad.