I had great sounding bass from Transformer HD DVD except for the Shockwave sequence towards the end of Chapter 1. When helipcopter decepticon is attacking the base, he sends out blue shockwaves. I knew my setup was working correctly since I was getting great rumble from the helicopter blades and all the explosions, but no audible or palpable rumble from the Shockwave as some posters have noted.
According to one poster, the reason for this is that there is no perceptible bass encoded into the LFE channel, only in the main channels for this effect sequence. I don't know whether this was intentional or encoding error.
I had my Denon AVR 3808 set "correctly" with Main speakers set to "Small" and Bass management as "LFE" and crossover at "80 Hz". With this setting, any bass frequency from the main channels below 80 Hz and alll LFE signals are sent to the subwoofer. However, this did not seem to be the case. I wasn't getting the rumble from the Shockwaves. So I set the Bass management to "LFE + Main". In this setting, any bass frequency below 80Hz from main speakers (regardless of whether they are set to Small or Large) are sent to the subwoofer. With this setting, I was finally getting both audible and palpable rumble from the Shockwaves.
So if you are not getting the Shockwave bass, check your bass management. In my case, I am convinced that it's a bug in the Denon receiver, since I should have gotten the bass from the main redirected to the subwoofer (since the main speakers were set to Small). The key is whether you hear the rumble from the blue shockwaves. Finally, I do think the audio mixer dropped the ball with the encoding by not including the low frequency effects sound from the shockwaves to the LFE channel.