Hi,
What i feel is the thread is simply asking you to let the speakers "burn-in" so that they reproduce the sound at their best.
Yes, this is an important factor and if you perform speaker calibration (automatic/manual) on an "out of the box" speakers/equipment, there would be some error.
Finally there may also be some phsycological reasons as well.
As for your subwoofer sounding flat, here are some points to consider:
-Is this a brand new sub, that has NEVER been used?
-Have you set the speaker settings and cross-overs correctly?
-Is the speaker connected correctly (audio and power)?
-How is the phase of the sub? If this is adjustable, please try adjusting the phase and the level!
I would recommend you to set the AVR to route both the LFE and main channel audio to the subwoofer.
I had to keep the subwoofer at the back side of my room because the sub was radiating sound "out-of-phase" the other speakers and my sub does not have any phase control.
If all else fails, you should try a replacement.
Thanks,
Nitin.