Happy to have stumbled upon this thread.. and i think i might be able to shed some light on the difference in "loudness" between PCM and Bitstreamed audio. It's the receiver.
I recently went from an Onkyo 674 to an Onkyo 805 after my 674 released the magic white smoke.
With my 674 there was a NOTICEABLE difference between the loudness when going from a Bitstreamed DD track ( or any other audio source for that matter) to the PCM 5.1 or Tru HD Track which was being sent via PCM. ( I have a PS3 ) The LFE channel also felt muted in the PCM track.
With my 805, i hear VERY little difference in loudness between PCM and Bitstreamed audio (and any other audio source). The fullness of the PCM track is absolutely there, its just the sound level is correctly interpreted somewhere? I have NO idea why this is, but my ears do not lie.
I have set up my system with an DVE disc and a Radio Shack SPL meter along with using the Audessy setup built into my reciever but more or less, just for the distances. The decible meter proved the Audessy to be off by about 2 or 3 db.
I chalked it up to being something different in the recievers. Keep in mind sound is a very subjective thing, but to me, the 674 lacked the punch in LFE as well as loudness when using PCM. DD loudness levels were more on par with the loudness of a DD track or cable TV volume.
You are most definately not imagining things, but i think your culprit is your AVR. Still.. loudness levels having to be adjusted hardly justify buying a new receiver.
Just thought i'd toss in my $0.02 in.