Doing the same.. trying to get my 4k JP on my lvl 80s. Can't say that I've heard of the problem you experienced, though, but it wouldn't surprise me with the amount of stuff Blizzard broke with this patch and has yet to fix.
What realms do you guys play on? I started out on Eitrigg and was there for about 5 years, then I moved to Kirin'tor where I had some other friends when my guild fell apart on Eitrigg. I'm on the Alliance side with a human mage as my main (Shinratensei), an 80 Shaman (Kusokurae) and an 80 Hunter (Talania) as my alts, then on Eitrigg I have an 80 Death Knight (Khaine) still that I use to talk to my old friends from there.