My newest character (Yua) has a Levels layer, this layer does not apply itself on load. Only when I make a change, and then UNDO the change does the levels layer apply.
To replicate: load her, and then re-size the nose or something. Then ctrl+z to undo. Suddenly the levels layer will apply.
It is really as simple as that. I can make it work consistently.
Fur sculpt tool affecting other parts
The sculpt tool projects to each facing surface it can find and applies the sculpt properties to it.
To replicate and see what I mean, remove fur using Gradient Fill+Length. Then find an angle on the character that you think will hit several limbs. Apply a beam of sculpt fur by just clicking once. Rotating the camera around to see where the fur has been applied and you will see that all surfaces facing the camera (and your target) has been affected.
A better example is to aim at the head through the arm.
When you apply sculpt fur property to a limb with nothing behind it, it will only affect the facing surface. Lets say you put fur on the leg, you wont affect behind the leg. But if that leg had another leg behind it, you will affect both legs from the same angle.
I knew there was something weird happening, but now I know why. If you can fix this, then you will also fix the FPS drop that it causes when you affect several limbs at once.