Bruce Lytle, welcome to THR.
For me, running a few hundred cycles through the Pro Auto Disk with W231/HP38 sufficiently coat and lubricate the moving surfaces. I use W231/HP38 in all new Pro Auto Disk setup as my "break in" powder.
For one thing, I notice that the turret goes up and down a bit when cases go into their dies. My thinking says this is not a good thing, as far as stuff jamming, bullet seating depths, case expansion, you know... So I've shimmed up under the lugs of the turret with feeler gauges (for now) to take the slack out. .
This play is not a problem as the final dimensions for case expansion (flare) and bullet seating depth are determined always with the shellplate carrier pushing upwards with the bottom of the turret lugs engaging the top lugs of the frame - so the amount of play has no effect. You having shimmed under the turret simply engaged the lugs sooner, but this may pose a problem explained below.
This way the turret is in the same position every time.
Actually, having some "play" between the turret and the frame has its benefits. Some reloaders experience shaving of case sides when alignment between the sizing die and shellplate is not straight. Pro 1000's play allows self-aligning of case/shell plate to sizing die/turret as the case enters the die opening.
One thing that will affect the final dimensions of case neck flare (expansion) and bullet seating (But this applies to all progressive presses), is when you have less than full shellplate (say 1 case vs 3 cases) applying even pressure on the shellplate, there will be some deflection (tilting) of the shellplate to very slightly vary the case neck flare/bullet seat depth. I always set the bullet seat depth with station 1 resizing a case and station 2 flaring the case neck as seating the bullet alone in station 3 produced different seating depth. Of course, each time you check the bullet seat depth, you need to use another unsized case in station 1 and unflared case in station 2 so as to apply pressure on the shellplate as reusing sized and flared cases would not apply the same pressure on the shellplate.
Another thing is that you'll notice some variations in bullet seat depth of your finished rounds ever so slightly (say around +/- 0.0005" or more). This is normal for cases that have been reloaded several times as case length will not be the same. Different length cases will affect case neck flare amount and bullet seat depth.
I would recommend you use the press without any shimming. If you are curious, make some test rounds (with same length cases) and see if the "play" makes any difference you can measure.