Here's a good article, an old one, I stumbled across that clearly explains what was at issue in the now-decided religious liberty case, Hosana-Tabor vs. EEOC. And here is the article that states Obama called Archbishop Dolan to tell him of the HHS decision. I didn't read this anywhere else. The article also states that Obama had assured Dolan in a previous meeting that Dolan would be happy with the results of the conscience rights decision. Obama certainly has a strange take on life as the president of the U.S. Seems it's always opposite day for him!
For another perspective on the matter, read Fr. Rutler's parish notes.