The charge weighs what it weighs... and what's important is that the dropped weight is consistant from one charge to the next... And the AutoDisk system isn very consistant, especially with ball powders.
What your experiencing is very typical of new reloaders who are starting out with Lee equipment, and that is the tabulated VMD values always give light charges....
There's two reasons for this....
1. Lee gets more new reloaders set up economically than any other company, and they support the concept of using volume only powder measurements. So the VMD values are conservative and (imo) intentionally drop light, assuming that many new guys aren't buying a scale.
2. The actual VMD will vary from lot to lot and also with the environmental conditions (especially humidity). So again, Lee publishes conservative numbers.
What new guys don't realize is that the tables are not intended to yield a spot on charge weight, first try every time. Rather, they give the guy without a scale, a safe charge. And they get everybody else in the ball park.
There are no shortcuts to getting spot on charge setups with the Auto Disk system....
First, you have to have an accurate scale. And imo, the Lee safety scale is not a bad one to start with. Though it is slower and more cumbersome than a good balance beam, they are amazingly accurate. I've tested mine against a $500 lab. scale at work and it is right on the money.
Second, you have to take and keep good notes. Then you will be able to repeat your desired set ups without going through multiple iterations.
Rule of thumb with the Lee table is to start one or two disk sizes higher than the table shows. And weigh a series of charges.
So in summary, it's got nothing to do with the powder drop and everything to do with the tables being conservative.
We really could use a sticky on this question, as it has to have come up a hundred times.