Okay. I've talked about this with a guy on another form who actually works on liquid cooling related things and he says CPU blocks work better when they're the first thing in the loop, so I'm going to do a bit of re-plumbing tonight. I write an exam in a few hours but after that I'll be able to plug away at this. While I'm re-plumbing I can take the waterblock apart, take a look inside and re-seat it properly.
I tried reseating the block with it still attached to the loop so I wouldn't need to drain and check for leaks again, so I couldn't really see what I was doing half the time, the tubing kept moving the block around until I screwed it down, etc, etc.
I haven't had the time to do very much yet because of this nasty exam I'm working toward but thank you all for your advice anyway. I've got it all written down, and I'll be back tonight with the results. The problem is I have so many things to try, I won't know what did the trick if I fix my problems.