Two things to keep in mind...
I like to calibrate the header with a block of wood under the feederhouse faceplate. When calibrating, you need the height sensor to fully compress, but no more than that. Movement between the header pins and the feederhouse is not good during calibration. The proper block of wood can really help make a good calibration.
Also, with a MacDon, or any other flex header, during calibration, you don't want the header to bounce up while it is "learning" This can easily happen if the large springs are set too tight on the MacDon. Calibrating with crop on the header and/or the reel fully extended can help prevent the header from drifting up while calibrating. I prefer to calibrate with the driveshaft unhooked. The two above procedures can really make for a good cal on our older 740.
Also, if you do a good calibration, and the combine tries to slam the header down when you want it to automatically lower, is the header drifting up while it is in the air? You don't want the header to drift up on its springs while automatically lowering. When it does, the combine thinks the header has made contact with the ground, even though it hasn't. Then when the header drops again from its springs, the combine tries to slam it down because it isn't sensing any ground. This can be fixed by reducing tension on the four large springs. I assume you are preparing for wheat, so you won't need much tension anyways.