A case full of 3031 under a 405gr is going to be a pretty stiff load so that makes sense. Having unburnt powder seems odd though. I've used 3031 a little but was using it for lower pressure loads (maybe 2/3 to 3/4 case full; don't remember the exact charge weight) and never had issues with unburnt powder. 7828 leaving a lot of unburnt powder makes sense since it's a very slow magnum powder so would want higher pressures to burn properly (at least a level 3 load if not higher which isn't safe at all in a lever rifle).
Did you chrony any of the loads? Recoil is directly related to energy produced, regardless of pressure produced, so having a load with excessive recoil to get it to hit PoA compared to lower recoil with a different powder sounds really odd. Could have been something weird going on or maybe the rifle just responds differently to the two different powders.
Even with a full case, unless you're running a compressed charge already, the powder will still get compressed if the bullets are set back in the tube under recoil. I only shoot paper patched in single-shot rifles so have never had to deal with PP'ed bullets getting set back under recoil.