GL_POLYGON not filled properly?

Answer 1

I think disabling GL_POLYGON_SMOOTH would fix that, but you'd lose the antialiasing. FSAA would work as an alternative, but it'd be slower.

Edit: looking around, there are a lot of examples out there using glBlendFunc( GL_SRC_ALPHA_SATURATE, GL_ONE );

Answer 2

GL_POLYGON_SMOOTH is an antiquated and slow method of polygon anti-aliasing. It also results in the problem you see above.

Using the Multisample buffer extension is the best way to perform fast anti-aliasing on modern machines. Read more here.