It seems that the cause and solution have been ironed out, but there is still one interesting detail that is not explained.
The bitterness is caused by an unbalanced sulphate:chloride ratio and perhaps too much sodium. In my experiments I have seemingly been able to correct this. The oddity is that it seems most people don't really experience the bitterness until after carbonation.
The question is, is this an effect of the flavor enhancing nature of CO2, or is this an effect of time that happens to coincide with when most people carbonate their beer.