I missed their denial. Can you tell me where I can read about it? AFAIK, they have neither acknowledged or denied a problem.
I'm confident these remaining 301 issues will be resolved in the next update. When Google did monthly updates, obviously they could and did resolve issues more quickly. IMHO, it's unrealistic to expect them to rearrange their update schedule for a few disgruntled or impatient webmasters with a few 301 problems.
I doubt that we're seeing an intentional penalty - more like a tangled up snafu. Clearly something about Google's basic approach, something really rooted in there pretty deep, has made it very challenging for them to deal with 301 and 302 redirects. For a long time they ignored the problem. Now they are doing this and that, but it keeps tripping problems.
That's my sense too, and I'm certain GoogleGuy read that thread. Patience! :-)