Patents are examined by people who are educated, but not necessarily business-minded. They get paid the same whether they grant every patent or grant no patent, but they catch hell when they grant a patent that shouldn't have gotten through, so this puts them on the conservative side.
I'd guess the non-patents you cited were on the "obviousness" grounds, though I'd posit that up until 5 years ago it was more a matter of getting a lax examiner and being good at negotiating than how obvious such things were or not.
Patents aren't as ironclad as some would like, anyway. Even if they had gotten those patents, a judge with the equivalent of a 1950's high school education would be making the decision on their technical merit, and whether X infringes upon Y. Good stuff gets struck down and bad stuff stays up all the time.
While waving your patents in front of the competition in order to get them to back down, sometimes it's like you have the US army behind you, and sometimes it's like you have the salvation army behind you, in terms of how much threat your patents actually pose from a legal perspective.