The MQA decoding situation is still pretty confusing. I have read a little about it and I'm not sure what level of decoding you get through different software and hardware combinations. If your DAC is telling you 44.1, I'd say that's what you're listening to.
MQA says that there is some benefit realized when files are remastered (or whatever the correct term is) for MQA, so maybe that is the improvement you are hearing.