We study the late-time ( t > 0.5 days ) X-ray afterglows of nearby ( z < 0.5 ) long Gamma-Ray Bursts ( GRB ) with Swift and identify a population of explosions with slowly decaying , super-soft ( photon index \Gamma _ { x } > 3 ) X-ray emission that is inconsistent with forward shock synchrotron radiation associated with the afterglow . These explosions also show larger-than-average intrinsic absorption ( NH _ { x,i } > 6 \times 10 ^ { 21 } { cm ^ { -2 } } ) and prompt \gamma -ray emission with extremely long duration ( T _ { 90 } > 1000 s ) . Chance association of these three rare properties ( i.e . large NH _ { x,i } , super-soft \Gamma _ { x } and extreme duration ) in the same class of explosions is statistically unlikely . We associate these properties with the turbulent mass-loss history of the progenitor star that enriched and shaped the circum-burst medium . We identify a natural connection between NH _ { x,i } , \Gamma _ { x } and T _ { 90 } in these sources by suggesting that the late-time super-soft X-rays originate from radiation reprocessed by material lost to the environment by the stellar progenitor before exploding , ( either in the form of a dust echo or as reprocessed radiation from a long-lived GRB remnant ) , and that the interaction of the explosion ’ s shock/jet with the complex medium is the source of the extremely long prompt emission . However , current observations do not allow us to exclude the possibility that super-soft X-ray emitters originate from peculiar stellar progenitors with large radii that only form in very dusty environments .