We’re also experiencing this issue, where tests show as green on travis-ci.org but the status indicator on github is still showing as pending (support email sent separately).
My first thought is that maybe it’s a repeat of the April api limit issue linked to above, but the status page reports no github problems so perhaps not?
Browsing these forums it seems like there might be a few concurrent problems going on – e.g. build queues.
It is (currently) unclear to me whether the queuing is part of this though (given that builds have run / completed, just not updated on github).