I went through somthing similar to what you are experiencing but to lesser degree it seems. I tried the sea hare route and similar results as many others; the power heads got them. I will vouch for Drew's sea hare though, it did a wonderful job after I rescued it from a power head.
Its encouraging to hear that the areas your urchin has cleaned are staying cleaned. So far, my tank is staying GHA free after I eventually over hauled it. My problem was an extreme bio load, which I've since cut in half. How many fish do you have in your tank?