Natural variation?
Assuming the SB card in your Amiga isn't damaged in some way (I'm assuming that because you haven't mentioned any inconsistency or unreliability in the sound level, just that it seems low) then it's either:
(a) You have one plugged into the headphones output, and the other plugged into the line-out. These give very different output levels.
or
(b) Software. I don't actually know much about the software used on modern Classic Amigas, but if it's through AHI, that probably has it's own mixing panel / volume preferences. Also check your mixing & volume settings under Windows, keeping in mind that the default is usually 50% for most of the controls.