I do have an Analyzer Pro and have never had any problems with the calibration procedure. However, I prefer a continuously graded step tablet, where I can measure the ISO-R value with a simple ruler.
You must first calibrate the offset (first non-white) and then the contrast settings (last non-black).
What kind of light source does your enlarger have? Can you state your exact procedure? Are you calibrating for VC or graded paper?