I have two accounts but for the past half year or so I could update like this no problem. I would log into one, and it would only download the updates for that account if I click download all, then log into the other one, repeat the procedure (that is also how updates are handled on the iPhone). This problem did not occur until a few days ago (when I first posted). Turns out I can download them individually (for the first account and then the remaining ones belonging to the other one in batch), but honestly? It's a bit hard for me to remember which account I used to buy which app (so I have to try them all and not mistakenly click buy to buy an app again that I already bought on the other account - because there is not actually a way for me to tell which ones I bought on which account at first sight), so this is not a permanent solution for me. Why does iTunes handle updates differently all of a sudden? It was much easier and more straight forward before. As far as I remember, the number of available updates represented all updates available but then it would only show the ones available on the account I'm logged into, and then display the others when logging into the other account
The post above worked when I had the issue too - thanks!
Although I've only had one account, when Apple forced me to convert to the new Apple ID, it considers my computer as having two accounts. In order to download, I had to type in my old account info and recall the old password. I should have ignored those Apple reminders to update my apple ID!!
If I go to my purchase history none of the apps I have purchased are listed there. I have a feeling that's the problem. I don't know why they're not listed, but if they're not a part of my purchase history, when I try to update, it doesn't see me as having purchased them and won't allow me to update. I repurchased an app having been told I wouldn't be charged, but I was.
omg, that's it. I just figured that out too. When I went to my purchase history and saw that there was practically nothing there, it finally dawned on me. Why the tech people at iTunes don't know this is beyond me. Thanks for confirming that this is the problem.
So, after many weeks this appears to have been fixed by Apple, as iTunes is back to the way it was before this issue occurred. Now it only displays the apps for the account I am logged into, and I can download them all in a batch. Great news.