Wow, you guys must have bad luck. I lived in Jax for 6 years and traveled constantly to SC to visit my family (Charleston), DHs family (Brevard, NC) and I never had long, long delays like that except the Sunday of Thanksgiving weekend which is to be avoided at all costs! I did, however, commute during rush hour for those 6 years and that was the absolute pits. Whatever you do, avoid 6:30 - 9am and 4 -7pm on weekdays. And, it's not a bad idea to go ahead and take the I-295 bypass around downtown because I-95 makes that ridiculous merge downtown and that is frequently slow. We lived south of Jax right off 295 and I often went that long way around to avoid traffic.
Hope you have better luck (and hope we do too, now that we live near Savannah and have to drive THROUGH Jax instead of leaving from the southside.)