Dolby Digital vs. PCM - PS3 & Denon AVR1909

[Radcon]

What sounds better, Dolby Digital or PCM and what's the best mode to run Blu-Ray in? I recently purchased a Denon AVR1909 (provides True HD, DTS HD) and did a trial run with "The Wild" and "Troy" in PCM vs. Dolby Digital (both have uncompressed PCM soundtracks).

While PCM sounded a bit more distinct, Dolby Digital seemed to have more presence, particularly with the bass. Was this just due to a difference in volume or do the sound engineers tweak the sound for Dolby?

I'm also confused by the difference between using the Direct mode and the Pure mode. In the Pure mode, all AVR decoding is turned off, but should it matter with PCM?

Also, I am using with five speakers in 5.1 mode, so if I use the Pure Mode, will the receiver send all the information to my 5.1 channels, or am a losing two (7.1) and thus the difference with Dolby Digital (I don't think this would explain the difference in the bass response)?