I came across the bitterness quite frequently, but in my case it turned out to be not frying the onions in hot enough oil before the boiling stages of cooking my base which is based on Darth's base. I don't think of it as biterness though, more a 'harshness' that catches you at the back of your nose.
If you think about frying onions for a burger or hot dog, there is never any harshness, just lovely oily sweet fried onions, so i concluded you have to fry them at quite a high heat and in small batches before adding them to the boiling pan.
Just my experience.
steve