Having two different ground planes on the same layer Eagle
The problem is that eagle does not know which polygon to fill first. For some reason, it doesn't care and "merges" both.

The correct way is this:


Draw both polygons
Assign different net names to them
Assign different ranks to them (e.g. in their properties). Polygons with low rank will now be drawn first.


Here is an example with two overlapping L-shaped polygons:

Polygons before ratsnest:
 

Though different net names are assigned, the polygons are fused. At least, the design rule check will complain:


Setting upper left polygon to rank 1, lower right to 2, and applying ratsnest. The upper left polygon is drawn first, the lower left takes what's left:
 

Changing upper lefts rank to 3, the lower right polygon now is drawn first: