I run the Smarty Jr. on my '06 without any problems. I think maybe you are confusing it with the TST Powermax CR which had problems with the later '06 trucks.
2006 3500 Big Horn DRW Auto QC Silver, 4x4, Billet single disk TC, Transgo, lots of billet parts, PacBrake, Max-Brake, Smarty jr. , Quad boost fooler, FASS 150/150, gauges.