Eagle: polygon pour leaving funny blank areas
This really looks like you have something in other layers that is preventing the polygon algorithm from filling the entire area.  Obvious suspects are bRestrict and a messed up outlines layer.

The way to find this is to turn on all layers.  This is done with DISP ALL, if I remember right.  That will show a bunch of superfluous stuff, but it shouldn't be hard to look for edges where there should be none.  I'd start with DISP NONE BOT BREST OUT first and examine it carefully.