Interesting, I have this problem with probably half the curries I make. I tried the undercover base last weekend and wondered if it was that, but now I'm thinking maybe it's something else I'm doing   

I had a sour after taste and then realized it wasn't the curry but fags and cider to blame....

I had this problem at the beginning too. You can try the sweeter spanish onions, or, what I do is to spoon off the surface froth/layer duting the boiling stage.
I think many of the bitter chemicals are in that area. It helps anyway. Try not to stir that layer back in.

To the OP - what quantity of onions are you using? You listed all your ingredients but just "onions" so its impossible to judge whether the recipe is anywhere close to the right balance of ingredients.  Too few onions in proportion to your other veg could give you a wrong flavour.

My other suggestion which you could try - see if discarding more of the root end of the onion helps with improving your results. The bitter flavour compounds are concentrated in the tough area towards the root end of the onion and although I would think they should get converted in the cooking process, maybe this is where your errant flavour is coming from.