From what I can remember its goes something like this
when Qui gon died there was balance in the force so he was burned on the Pior which is jedi tradition
then later on there is imbalance caused by the Jedi Purge, so Qui gon finds a way back via the force as a spirit (the scene was never completed for the film.)
the imbalance is so strong that OBI & Yoda disolve into the force at the time of their deaths
when Vader dies he has restored the balance to the force by killing El Sid, & as a result luke Burns his remains as is the tradition.