how much beer is going into the keg? and what size keg do you use?
Going on a hunch here, at work when we will only put 1500 gallons into the 2000 gallon brite tank, it is likely to over carbonate because of the significant headspace in the tank.
The same principle applies with 5 gallon kegs. The carbonation will be drastically different if you fill your keg with 4.5 gallons vs. filling it with or 3.5 gallons. are your dark beers boiled off more, and not enough volume goes into the keg? just guessing here.