Which iPad PDF viewers (annotators, readers, whatevers) give a faithful rendering?
It seems to me that maybe not enough Fonts have been embedded in this ("old") PDF. I downloaded it on my Mac, opened it in Preview and exported it under a different name (without changing anything else). 

GoodReader on my iPhone now shows the alpha´s correctly. Inspecting it with Acrobat Professional now shows more imbedded Fonts than before (and of course a newer PDF standard being used).