Where did my lows go?

[Feanor]

My room is no more than 12 feet long and I get about 40Hz @ -3dB from my small standmount speakers.

You may feed your system 40 Hz and you might get -3 dB. But here's the catch: you might not be hearing a pure 40 Hz sound. Instead you are getting distortion.

In a rooms too small to reproduce a certain frequency, all that power you're feeding has to go somewhere. It creates distorted sound at a higher frequency than the input signal.