I have rebased my branch. That's probably, why you get so much on top in your area.
The plot makes sense from my point of view, since the it is not guaranteed, that the best track has been set upstream. Maybe you intended to use muonBestTrack() instead of reco::Muon::muonBestTrack() in pat::Muon::embedMuonBestTrack()?

Anyway @bellan @slava77 , since I do not have access to LXPLUS right now, I'm gonna close this pull request and move to #733 with my fix included. That is the one for CMSSW_5_3_12 then.