jen,
i don't have experience with paraffin or dipping boxes.
first off, over time the bees manage to wax the insides of any box (and propolize) just give them time to do it. a little help to dipping them wouldn't hurt.
2 bucks a box, that seems fair, might have to do it again at some point?
painting boxes? i don't paint boxes, as you said they peel. pine has knots that sometimes will 'eek' through the paint or any stain. these knots need to be sealed, and oftentimes undercoats of whatever do not seal these. i use something similiar to parafin to seal the knots, and use a good primer and i STAIN my boxes. i use either waterbase or oil stain. works for me, no peeling paint, and don't have to stain them again for some time. less work.......
good luck, let us know how it works out for you.