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GLSL and alpha problems

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I'm having trouble with the alpha channel. I'm using GLSL and framebuffer objects for rendering to texture with alpha components. Whenever I read back the data, the highest order 8-bits (alpha component) are all 1s, however the other components are correct.. This occurs when rendering to a framebuffer object as well as the main framebuffer. Using any GLSL fragement program, even as simple as just an empty function with "gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);" will yield all 0s except for the alpha component's bits which are all 1s. The textures (color buffers) for the framebuffer object are RGBA, as well as the main framebuffer being RGBA. Anyone have any idea what I may have done, or not done, to cause this?

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