The problem is explained here: http://theoldreader.yuku.com/topic/113#.UakOj9eVtQI
Basically, I made a bug report thinking The Old Reader was not parsing feed URLs correctly. They replied and said getting the feed URI from the <link rel="self"> tag is the correct URI according to RFC 4287.
I wanted to subscribe to an specific tag (http://danbooru.donmai.us/posts.atom?tags=konpaku_youmu), but checking the source code, it has the <link href="http://danbooru.donmai.us/posts.atom" rel="self"/> tag, which means putting the full URL in The Old Reader (and any RFC 4287 compliant reader, I suppose) subscribes me to the "general" Danbooru feed (http://danbooru.donmai.us/posts.atom).
Is this something that can be fixed on Danbooru's end, or do I have to ask the Old Reader staff to do something about this?