Hi there,
I have a very similar problem: a number of pdf files that I can see perfectly well in Safari/GoogleChrome do NOT show correctly in Preview or ANY iPad app I have (Notability, Adobe, PDF Expertm iAnnotate, Dropbox etc.).
The problem is that punctuation -- with the expection of periods or bolded text -- does not show properly. For example, commas and quotation marks to not show, and some numbers to not show.
Moreover, once I have annotated/viewed the problematic file on the IPad and resync to dropbox to view on Mac vis Adobe (which I do with most pdf files with no problems), I get an error message upon reopening the pdf file saying "Cannot extract the embedded font 'FAFWQV+--unknown-2--'. Some characters may not display or print correctly." (the 'quoted' text changes each time). When opening in Preview, no error message appears, though the fole is still lacking punctuation etc.
Here is a link to one problematic pdf:http://niis.cass.cn/upload/2012/12/d20121201200145301.pdf
NB: the file is in Mandarin, however I can successfully open/edit/annotate/sync other pdfs using Mandarin font so I'm not sure if the language is related to the problem.
I would be extremely grateful for some help with this please!
Thanks!