I think the clear always sinks into the grain of the wood or any micro-crevasses there may be. In addition, by sanding the upper surface, you created a contrast that makes the lower levels of the clear coat more obvious. It is just a theory...
If you look at pinball machines from the late 70's or early 80's, they were never slick and smooth or intended to look like a glass surface. That trend to turn every poor quality wood box to look like a metal box or a marble coffin is ludicrous in my opinion.
Yves