[allovertheglobe]

PDFs are a pain because the format is so variable that it allows for a lot of abuse.

You are in a good position to answer your own question since you have both a bad and a good version of the same document. Try to compare them, filesize-wise of course, and also by looking at the more advanced information (in Acrobat maybe) like which application was used to create either etc.

I would be interested to learn more about this myself.