this has to do with the gammtone filtering of human hearing
other as commonly assumed the ear is sensitive to phase,
or rather: to phase alignment
in hearing, time and frequency have critical resolution
here you see an example of a gammatone filterbank output:
http://www.southampton.ac.uk/aim/aim-figures/bmms.jpg
you clearly see the onsets of the waveshape
these are processed by the brain in a correlation like fashion,
where the correlation gives (part of) the pitch impression
when the phases are not aligned, and the frequencies are slightly drifting
it sounds very different (for these low pitches you mention)
just send your low pitched sound through a long and dense reverb
to note the difference
in addition, pitch is perceived by the spacing between harmonics,
(though you cant seperate that property from the time correlation)
so even if the fundamental is missing you perceive the same pitch