When you say pure direct 2.1 do you mean that the sub woofer is getting a signal when you put the receiver in pure direct mode?
Stereo/ Straight (and other variations) 2.1 means the signal is being processed.
PD/D 2.1 means the signal is bypassing all processing and the analog XO sends the bass signal to the subwoofer output.
For example, I sing karaoke in my living room using a Denon 3312 and Yamaha sound mixer.
The music goes through the Denon AVR, then goes to the Mixer, but the Mic is connected to the mixer.
When I use Stereo Mode 2.1 (for the bass), the music has to go through processing (DSP), instead of bypassing processing and going directly to the mixer. This causes the music and mic to be out of sync in the form of reverberation/echo/lag.
However, when I use Pure Direct or Direct 2.1, the music and mic is in perfect sync because the music is bypassing the Denon DSP and going directly to the mixer. However, I still get all the glorious subwoofer bass!