iOS 6.1 is out and it did NOT fix the problem.
Sent another bug feedback to http://www.apple.com/feedback/ipad.html (and yes, it's a bug, because this USED to work!).
I went to the japanesepod101.com message board where this issue is discussed to let them know and have them send feedback.
If only one or two people are complaining about it they won't do anything.
I loved my iPad (this was the whole reason I bought the thing), but now it's not working for the function I bought it for. I have all my friends telling me I should have gotten the Android tablet. I'm startng to think they were probably right.
Sorry, just really upset.
I haven't been able to copy a single word/character without it selecting an entire sentence. And I hate how Adobe reader works. I bought GoodReader to manage my large number of pdfs and it works perfectly - and I spent a lot of money on it too. I don't like Adobe Reader, I don't like how it works when scrolling through the pages of the pdf. Part of the reason for that is I'm not used to it and it doesn't do as much as GoodReader does.
I don't know what irritates me more - that Apple broke this functionality or that GoodReader is perfectly happy to keep their application broken, waiting for Apple to fix what THEY broke.
I just wanted to let everyone know - japanesepod101.com went and redid their pdfs and now the Japanese characters show up in iOS 6 and GoodReader (or whatever your reader of choice is on iOS).
I went back and looked at previous lesson notes - if you don't see the red semicircles on either side of the front page, then it's the new format that will work on iOS.
Re downloading them now.
I found that this was fixed in iOS 7 and wanted to make a note of that. This was after Japanesepod101.com kindly embedded the fonts in their lesson notes.
I have a few of the uncorrected pdfs left on my iPad and now they work under iOS 7. Took long enough, but it looks like it won't happen again - until maybe it gets broken again in iOS8.