Looks like DirecTV is now feeding WPSU and WKBS in 720p. I noticed this after midnight on Sunday morning. I haven't yet seen any HD content, but will be checking out WPSU in primetime tomorrow night, at least, to see if they feed PBS HD. Both stations were running local programming at the time. The aspect ratio appeared to be Stretch-O-Vision, even after switching on 'Native' on my HR20.
I wouldn't expect WKBS to be feeding any HD anytime soon.
Now all this leaves in 480p is WPCW.
I just checked this out on my TV and found that both WPSU and WKBS are still 480i.
You should double check your settings. Even if you had it on Native mode, if you didn't have 480i and 480p checked as available resolutions, it would upconvert.