Is this a subwoofer issue or just

If one were grading this as a science experiment the jury would still be out b/c of too many variables.  Different amps will have different Damping Factors (grip of the low end)  Practically speaking, what this means is that the sub working off an amp with better grip will need less help from the sub and it won't be a fair A/B if the sub is crossed or high passed at the same level.

You didn't state if you changed speaker placement or sub crossovers for each amp.  To be fair make a decision after truly optimizing each setup.  

no change in speaker placement or crossover or anything else.  

Amp A might require a different integration with the Totems and the sub.

@jastralfu  +1

Amp A is the keeper, the sub is an irrelevant variable. Keep A, and spend more time on the integration as suggested.

@dunkin 

how is the sub connected? 

@zlone +1

Thank you all for the help.  I will try a different sub integration with Amp A.