Pcdmis has, as part of DCC Circle, a choice for entering in the pitch of the threads. This will cause the program to measure the circle at different depths thus keeping the probe in contact with the same part of the thread, either the tip of the thread, the edge of the thread, or the depth of the thread. You can't really set which part, but by using the pitch, it will always hit in the same area of the thread. If you don't have this, you can always use the biggest probe that will fit in the hole to measure it, thus reducing much of the error for contact location on the threads.