Okay, I made some progress on this and pretty much know why I was having so many problems isolating what was causing the low core loading. I'm using two scenes now: the original scene I have called "SlowCloudsComplete" and a test scene called "SkyGrass".
The original scene is too large to upload here. It has 29 populations, a large 8192x8192 World Creator terrain, a stock atmosphere, the "Large, fluffy cumulus.tgc" file from the free TG4 presets package. It is set to render at 3840x2160 (4K) with all cores and 64 threads. When populated, TG uses 7.1GB. When rendering, it tops out at 28.7GB. The render will successfully complete in 11+ hours. If I change the cloud tgc out (it's a Cloud layer v2) with a Cloud layer v3 with data the same (as much as possible) with the v2, the scene renders in 3+ hours.
The test scene is the same tgc cloud file and atmosphere and one large population -- the grass clumps. Pretty simple setup (I uploaded it in one of my posts above.)
For some reason, I could see the same core loading problem in the test scene as I did in the original scene. I tried it several times and finally uploaded the test scene to see if others saw the same problem. The next morning I checked this forum and Oshyan said he didn't see the problem. So I loaded the test scene and sure enough, it rendered normally at 100% until near the end where there isn't much work for all the cpu's.
This morning I tried something different. I loaded the test scene and it rendered at 100%. I loaded the original scene, without exiting TG, and the 34% loading in the cloud area of the scene was there. I again loaded the test scene, again without exiting TG, and the 34% core loading problem was there. I exited TG and loaded the test scene and it rendered at 100%.
So I'm pretty sure that's why I kept getting different results. The problem scene seems to do something internally to TG which only reloading TG seems to clear (at least that's my theory for now.)
I'm going to try some rough memory usage tests to see if there's a difference when simply reloading the different scenes and reload TG and then the scenes.