Actually, I’m not sure this problem is related to 12.1. I’m running iTunes 12.0.1 on a Windows 7 machine, synching to a Touch iPod. The same thing happened to me, but just with the Snap Judgment podcast. I was able to redownload old ones, but they won’t synch. And if I try and do it manually, they show as grayed out in my library. I was able to work around it by downloading directly to the iPod. The new ones synch fine. A similar thing happened with a new subscription, to ReSound. (Third Coast). Can’t get old episodes to synch, but they download fine to both iTunes and my iPod. New episodes synch just fine. Both of those use SoundCloud, so maybe it’s an issue with them?
Also, a couple of weeks ago NPR changed their feed which messed with naming of some of the podcasts (and eliminated the Most E-Mailed), but none of them have any trouble synching.
FYI, I found this post when looking for problems with 12.1 & podcasts before downloading it, but I definitely won't be rushing now!