With out knowing the system layout and all the components in the system its a crapshoot at best on why.
Maybe something with your radio settings got changed, subwoofer output volume, bass settings, or crossover on the headunit got changed since you set it. Maybe you set the amp at a different volume setting, maybe the remote bass knob wasn't all the way up, maybe your batteries are not fully charged and its creating less power.
It should have nothing to do with it being a lithium or agm issue.
There's so many actual possibilities to why its testing different from when you first set it up.