Jack tells Jen that the phone call from her parents has been 5 years coming. Seasons 1 & 2 combined were one year, 3, 4, & 5 were each individual years. Therefore, though it's the end of the 5th season, only 4 years have passed in the show.
Joey asks the guard at the prison why her family wasn't informed that her dad was paroled, but they weren't informed the previous time he was paroled either. They only found out when he showed up at their house. There is no reason for Joey to believe they would have been informed he was paroled this time.