I doubt there is anything wrong with your truck, exhaust and intake amplify the mds transition, you could disable mds with the superchips 3865. I found the surge and sound unbearable so i disabled it.
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06 RAM QC 1500 HEMI MODS: K&N 77 cai / 3865 flashpaq / jet 180 t stat / 3" catback flowmaster / rancho rs9000 shocks / pioneer head unit / infinity speakers / sub amp driving 2 twelves / spray in liner / 5000k yellow fogs 
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