Allen Media Group did sign the show's host, Jon Kelley, to a new deal back in February. He does other work for AMG, including commentary on HBCU sports, and the new deal also gives him the option to executive produce new programming. I could see AMG produce some more episodes for next season with Kelley still in the fold.
I don't think Who the Bleep got much clearance on stations.
As for YBYL -- Leno did say he did not want to cross the picket line, but there was also some talk that he refused to take a pay cut to keep the show going.
JD