A couple of things suggest themselves as this sounds like it might be inconsistent distribution of crystals in the chocolate.
1) Keep the chocolate at the melted point for a while longer, 10 minutes? before starting the cool-down part of the cycle (when you add the seed chocolate). This will help to ensure that the chocolate is completely melted. Remember, the temperature is only being measure where the little sensor probe is located. Waiting a while will make sure that the chocolate is a more even temperature and that the crystals are all melted out.
2) When the temper cycle is over, do two things: a) stir the chocolate a bit to mix it, evening out the temperature and spreading the crystals around; and thenb) wait a while before starting to use the chocolate - remember, the temperature sensor measures the temperature in only one place.
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@DiscoverChoc