There's a ton of things that could cause the problems.
Lets start by measuring a the headspace length on a case fired in the Savage and compare it to that of a case fired in the Howa and them to a sized case.
Measured from the bottom of the case to the datum line.
Do yourself a favour and measure fired cases from both chambers and a sized case and compare them to each other.
Next up: the fact that only some of the cases wouldn't close, indicates spring back after sizing. This can be addressed by annealing and letting the case sit 2 seconds at the top of the cycle during sizing.
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