Thanks for the replies and suggestions - I emailed Mr. John East and he sent this reply:
"Hi Ben
Are you using the retro with the volume at max?
The J or U-Retro is not designed to be used in active at max volume especially if you have a lot of EQ dialled in. Many are used to using passive basses this way of course.
Remember that the retro volume control should be thought of more like a slider in a sound mixer channel strip, where it isn't the norm to have them all at max. The more EQ you have, the more they tend to be backed off. The retro has a lot of EQ boost capability, being a quite a 'sharp tool', and a single 9V battery isn't capable of giving anywhere near enough headroom, especially with really powerful pickups.
To set retro up with a rig etc:
* Go to passive mode with volume at max, with both pickups and set the volume of
the rig to a good level.
* Back off the volume and then switch to active.
* Set the EQ and adjust the volume to taste.
* Backing off the volume effectively creates more headroom.
Please try as above. Very happy to look at your preamp if you think it has a problem.
By all means call me if that would help?
Best wishes
John"
Turns out when I backed the volume off before I didn't do it enough, this seems to have solved the problem Hope this helps anyone else who may have the same problem - although to be honest, it was really me just being stupid and not trying the easiest solution! :/