There are two possible causes for most of the variation--
1.) Most of the problems I'm reading about here with smaller charges of flake powders may well result from winter time static issues. Flake powders love to pick up static charge-Unique is about the worst case.
Search this forum and others for ways to minimize static charge or go to ball powders.
2.) One problem many people have is caused by not setting the powder-through expander die deep enough. If you don't do that, the auto disk doesn't move far enough over the drop hole in the measure and some of the charge can hang up on the lip of the drop hole. Users get into this because they don't want to flare the case too much--however, you have to set the die deep enough so the case will push up on the moving part of the die to work the auto disk through a complete cycle.
I am almost certain that this is the cause of a lot of the erratic powder drops. If I am careful to set the die right, even with Unique, I can throw 4 gr every time, without measurable variation. I throw 4.7 gr for 9mm with 124 gr. bullet and with a Lee Safety Scale or a Frankford Arsenal digital scale get no variation whatsoever.
Finally, the adjustable charge bar is not the answer to the problem. At small volumes it will also be erratic--and because of its design--basically a wide slot instead of a small round cavity--it doesn't fill or dispense well. Remember, you're trying to drop powder flakes out of a wide, narrow slot into a round hole in the bottom of the powder measure. The adjustable bar works best at larger volumes too and actually be more of a problem at volumes of .4 cc or less. It, too, will be affected by static buildup.
You can also help things by putting a powder baffle into the hopper--someone above referenced them. RCBS sells them and you can get them from Midway, etc.
The Pro Auto Disk Powder system is about as good as it gets. Just realize its limitations and the characteristics of powders. Flake powders can bridge, clump and charge with static.
Moral of the story--get a good powder scale and work up your charge drops. Forget what the Lee chart says--it is only a rough guide and was never meant to be the final answer. Powder density variation from lot-to-lot in and of itself negates much of what the chart suggests anyhow. And, Lee points that out in all its literature--always as a footnote.