Well, I ended up going home and plugging the guitar into my scope, ad sure enough, tiny output signal with both pickups, indicating... of course... out of phase. I guess the reason it tricked me, was because it still sounded alright if the neck pickup was not tapped, or if the volumes were up. Ahh well, live and learn.
After swapping all four wires on the CC, I re-scoped it, signals were all what you'd expect to see, and when I plugged it into an amp, the tone, definition, and dynamic control were all back the way they should be. So thank you VERY much for pointing out the (probably too obvious!) solution for me.
After our midweek gig, I've decided that these pickups are very well balanced, yes, the CC can be a little bright, but I can imagine if I were to loose the highs somehow, there would be some occasions when I'd be wanting to get more bite out of it, but not be able to, so I think it'll stay as it is for now.
One more questions though, Someone mentioned to me that if I find that one pickup is out of phase to the other (which it was) that rather than reversing the wires, I could reverse the magnets instead. I'm just wondering, is there any advantage to doing that, rather than just swapping the wires around? Because it's a 4 conductor cable on the CC, I've still got the coils being fed in the fight order (probably not the right term, but I'm sure you know what I mean), any reason I should consider this, or is it just achieving the same thing I've just done, but just with a little more fiddling around?