I would certainly be a lot more confident in the value the AquaController reports rather than the color matching kits. It sounds like it is properly calibrated. What is the alkalinity of your tank? What is the high and low pH of your tank over 24 hours?
I don't know if this is the case with your tank or not, but the color matching test kits are very inaccurate, and some are purposely skewed to read values higher than reality. Many tanks have pHs that run about 8.0 to 8.1 (especially Ca reactor tanks), but the books say the pH should be about 8.3. So the manufacturers skewed the pH tests to read .2 or .3 units too high. That way the user gets the results he is looking for, and continues to buy pH cal test X. Even if the tests are accurate you can easily get .2 pH variation in the reading depending on what type of lights (Sun, florescent, etc) you take the reading with.
Curt