iBooks not displaying PDF files properly. Help!!

Most PDF files open fine in iBooks on my new iPad 3. However, some show up with blank pages. Sometimes the first couple of pages are visible but at a very poor resolution so that the file is unreadable and then the rest of the pages are blank. Sometimes the whole file is blank. These are mostly PDFs of academic articles that I downloaded from JSTOR. Can someone please help with this?

I've looked online and found people reporting a similar problem 2 years ago. I this really something that Apple can't solve? Should I buy goodreader? I know it is only 5 euros but I don't want to fork out money if it is going to have the same problem.

Saving the ,PDFs again on my desktop, which is the solution suggested 2 years ago on the online forum I found seems a rather awkward solution for what must be a simple problem.

Is there another solution. Any help would be very much appreciated, thanks