Yes. Even though multiple frequencies are being played at even levels, when your room interaction is added to the mix some might be much higher and/or lower than others. Most people, except in the extremest of situations, will not be able to hear enough of a difference between those levels at individual frequency bands. With that much extra energy (or possibly not enough depending on cancellation/enhancement) the meter is going to misread as it will detect a lot of energy, even though much of it is at specific bands instead of even across the board.

Now if you had an RTA (real time analyzer) which would be able to show you the amount of sound pressure at different bands, you could potentially compensate for those issues, or even have a visual guide to moving the sub around until you find the spot with least problems. Most people do not have that capability as stand alone units that would have any reasonable bass accuracy are very expensive (>$1000), and easily available software solutions are not terribly accurate either, and depend heavily on the mic and other hardware hooked into your machine.