Sounds like a non-Bose'd head unit to me.
If thats the case . . . is it just changed with a Tech 2 ? Excuse my ignorance but clueless on this subject

Yes it can be checked or changed via Tech 2 but your need a Car Pass for the HU.
got the original VX car pass is that what you mean ? 
Tep,
Assuming thats what the problem is, which it well could be. On the Bose System, listening to a Middle of the Range' CD you can pretty much turn the wick up full blast with very little Bottoming or Distortion, if you getting early distortion or loud levels at low volume position level (use the steering wheel function if it helps as the Vol Knob on the HU just spins), then that would susest that the HU is kicking out higher o/p levels than it should, ie, non Bose configured.
It seems to be distorting quite early in the volume range. Had bose in 3 other omegas & never had to have the bass anywhere minimum. Whats worrying me is though if the HU was changed it would have different car pass details would it not ? 
No, well I say no, Ive been working on the assumption because its a 53 Plate it will be fitted with an NCDC, if this is the case then they would have used your Car Pass to pair the HU to your Display and maybe forgot or didn't know it hase to be configured for a Bose Set Up, then the Pass would remain the same.
If its a 2006 HU then they could just have fitted a standard Non Bose one, but that would come (or should have done) with a new Radio Code.