The CT scan of the heart is I am assuming an EBCT, which visualizes and calculates the amount of calcium in the coronaries arteries. There is good evidence that the more calcium one has then the more likely one is to have coronary artery disease, but sometimes these plaques don't affect the internal diameter of the vessels. For this reason the cardiolite stress test may be negative, since althought here may be calcium in the coronary arteries it is not significant enought o cause decrease in the flow of blood through the artery, e.g. usually less than 70%.
So the two test are actually looking at the same process, but at different stages and its different manifestations.