Well, as I explained in my review for Repo Man, there are several solid clues that the flashback was set in S3. Apart from the characterisation for Sam and Dean, there is also the fact that Dean doesn't have Ruby's knife and, as a friend pointed out, the Impala had its spotlights, which were last seen on the car in S3. In any case, the writers haven't been consistent where the missing year is concerned basically from S6 on. LOL