Thanks everyone for replying.
Over the weekend, using 1/3 depth into the slip sheet as a starting as a point as Framah recommended, I started making cuts, after changing start and stop points, then adjusting the depth, I finely found the correct blade depth, now my starting and stop points were very close to what the manual says there supposed to be.
As Framah says, its all about the correct blade depth. Also, being one with my mat cutter is how I feel about it now, as I made close to 100 cuts over the weekend.
Now, I'm getting good cuts every time, with just a very small amount of over cut that's hardly visible. Its so nice to lift the cut mat up and have the drop stay where it is. No more under cuts.
Its to bad that Logan couldn't have designed a way to tell how deep the blade is, as this is very hard to measure with any kind of accuracy, and from what I'm seeing, 0.010" makes a difference. I find that just 1/4 turn of the adjustment screw can make or brake the correct depth, but getting to that depth, is not east, but now I know this. Even after talking with there customer support, which was no help at all, they couldn't tell me this.