Yamaha RX-V663 very flat audio.

I want to make it clear from the bat, I'm no guru in HT nor am I good at setting the things up but I do know the basics.

Long story short.
Replaced my $900 AUD Yamaha RX-V540 4 year old amp with a new product in the similar price range, expecting similar audio quality but more imputs (being 4 years later)
I opted for the Yamaha RX-V663, again about $900 AUD - similar amount of component inputs, same video upcaling stuff (all output -> HDMI)


I am a gamer and my 360, PS3 and movies all simply sound flat and terrible on this new amp, specifically the bass on the unit.
I have only 4.0 speakers, however they were not changed in any way.

On both systems I've specifically told the amp that I have no center, no sub, etc. I've set the speakers to "LARGE" on both
I am not a huge bass head at all! (I live in an apartment) I hate disturbing people but the audio is just downright ...meek on this thing.

I had to set the bass to -10 on the old 540 because I didn't want to tick the neighbours off, on the new system it's as high as I can set it, still sounds awful.

Can someone give me some tips? Did they change some kind of DAC? is there cheaper components in this thing or have I set something wrong?
Please help guys, I figure this is probably the best forum on the internet to find someone who has experienced this.

Thanks to anyone who can help, I really appreciate it.

The bass on the 540 system was very loud and deep - I don't want to bug my neighbours.
The bass on the 663 system is so flat and lifeless that my neighbours will never hear the system anyhow.
I'm not even an audiophile thinking some kind of magic harmonic balance is off, it's just plain dead.
(If anyone here plays "Pixel Junk Monsters" on the PS3, when the boss comes at the end of the map, it is very meaty and bassy, on the new system it's dull)

YPAO has been run, it set the speaker volume and distance pretty well.
The mid range audio is relatively fine but the LFE stuff is just bunk.
I'm fairly confident the unit isn't broken, it's just a setting or a design flaw (?) but the deep rumble is noticably missing.

When you set LFE with no sub, it just sends all sub audio to all "LARGE" speakers, worked fine on the 540.

I've nearly had it a year already, just been lazy I figure it some setting, rather than a fault.
The bass is better if I set the whole speakers REALLY REALLY LOUD but before the bass was present at all times, if that makes sense.