Yes, I've been there before. You can throw that powder charge accurately and repeatably. You need to be patient and try different combinations.
There are several combinations of cavities that equal the same charge. Go to the Lee table that lists the volume of each cavity and write down various combinations, then try them all.
But first, a few tips:
1. Of course, always put the larger hole on bottom. It won't work with the large hole on top. You already know that.
2. Make ABSOLUTELY sure that you get a FULL stroke of the lever so the disk gets full travel, all the way back until it stops then all the way forward until it dumps down the tube. I know this sounds elementary, but I've made that mistake before, too.
3. Coat everything from hopper lid to charging die, using powdered graphite liberally. It makes the powder flow completely and helps kill static. I tried all the usual static remedies, but liberal graphite on all surfaces solved the problem permanently.