Auto-published updates do show up in feeds, actually. I've tested this extensively and it does work.
What has changed is the new "Top Stories" feed Facebook is showing at the top of the main page. Top Stories rarely shows posts from Pages, of any sort, unless they get lots of interaction. This limits the reach of Fan Pages in general.
Note that SFC doesn't have the same issue that has been widely reported recently with "auto-published stories get less than 70% of the likes" and so forth. That story was specifically talking about using third party applications like HootSuite, TweetDeck, and Networked Blogs. When you use those, then your stories get lumped together with all the other pages using the same applications.
SFC doesn't have this reduction because you're not using a third-party application, you're using an Application that you create yourself and which nobody else is using. Thus, stories published by your application *don't* get lumped together with a jillion other stories.
Now, you may have a problem where, basically, you're posting too often. If you auto-post a dozen stories from your site, then they're all going to get lumped together into one by facebook's app-merging thingy on the news feed. In which case, yes, you'll see a reduction in likes and comments because your stories are being hidden from the news feed. This is the same effect as described in the articles I mentioned before, except that you're basically doing it to yourself. In which case you should perhaps space out your posts a bit more, or publish them on a delay.
Bottom line is that posts made by Applications will get lumped together into one in the feed, reducing impressions. However, this only happens when they're made at close intervals of time. Space them out, or better yet space out your own blog posts, and you'll get more impressions.