I've used pretty much nothing but Unique in the original Lee Auto Disk Powder measure for 25+ years and as long as I stay above .4cc volume I've never had a problem. The "new improved" Deluxe model may have introduced a further possible restriction in the "cut-off" valve arrangement, but mine has worked fine for 4.3 gr Unique in .38 Special -- going lower for .380 caused problems so I went back to the old model for the turret press and put the "new" model dedicated to 6.0 Gr Unique for .45ACP on the Hornady.
Other people here have reported you need to just run some powder thru it to coat all the surfaces with the graphite anti-static that is part of the powder, then it will be fine.
Readings will be different if you just work the ram up to fill a case, weigh, and repeat compared to four handle pulls, fill a case, weigh, four handle pulls fill a case, weigh; as the vibrations from rotating the turret help settle the powder.
I definitely got lighter charges from the same Auto Disk on my Hornady Projector fixed head progressive press compared to it mounted on the rotating head Lee turret, but both were consistent when used, just a bit different in the charges thrown.
Definitely as benedict1 said, make sure the die is adjusted right so the disk takes a full stroke. I go as low as ~3.4gr Unique with the "old" model without problems in .380 loads, the "new" model was not consistent at this low volume.
--wally.