Yes, I had the duct connected to the... er... blue side... that's input, isn't it? not output? D'oh! Let's try that again... ok it's working now. I can't believe I did that - I do know what the colours mean, I just had a senior moment I think.
Now, the problem is that it is overwriting the liquid block every time and wasting my precious Liquid Essence (yes, it's MF2, but I added AM2). Not sure what I can do about that. Is there any way to detect a liquid block and emit a redstone signal to disable the activator?