B6 Avant dodgy sounding Bose sub

[no_idea]

I have a B6 Avant (2002) with Bose and the sub makes a 'farty' noise. It is more noticeable from outside the car. The amp fitted is the earlier black one without the audiopilot. I bought a new complete sub enclosure and swapped the speaker over but no difference.
Any suggestions?
Thanks in advance.