Same thing. I updated iTunes about 3 years ago & lost everything. I swore I'd never update again....but I did to whatever version changed the icon to the color red & have had problems ever since.
Can't get the podcasts I want to download checked and cannot UNcheck ANY podcasts at all - the only way to delete any is unsync ALL which removes ALL podcasts & start from scratch.....which doesn't work because you cannot check the ones you want - ad nauseam.
There are only a couple of discussions about this I can find here - even finding a discussion was hard unless I went through Google Search. It really surprises me there aren't more people discussing this and I sure wish there were a solution. Tried reverting back to a previous version of iTunes & it wouldn't revert according to the instructions I saw.
I sure wish some company would make a better line of products that actually work w/ problems being solved & leave Apple in the dust.