You might have the vertices defined in the wrong order, or the face culling set wrong -- see the bottom of
http://www.opengl.org/resources/faq/technical/clipping.htm.
There are lots of things you can do wrong in an OpenGL program to cause the problem you are seeing
Usually what I do is start from a known good program, then modify it step by step until I get what I want, verifying at every step that it still works. If you write too much OpenGL code at once, it's easy to get into a situation that's hard to debug.
If you want a bare-bones starting point, you might try my super-simple demo at
http://jogamp.762907.n3.nabble.com/Couple-of-questions-tp1889246p1913928.html. It draws one single triangle using vertex colors -- nothing can possibly go wrong!