Ive had a similar issue recently, dealing with alpha masking on a window. Turns out that not all video cards (namely NVidia ones) dont actually always support an Alpha channel in your main context buffer even if you request one. Which means even though you might be specifying 0 alpha for your clear command, because the buffer itself doesnt store an alpha, its always going to assume that its fully opaque. use glGetIntegerv with GL_ALPHA_BITS to find out wether or not your buffer actually supports alpha.

If it doesnt, then you are going to need to find an alternative. If you have a decent enough video card, look into the extensions for PixelBufferObjects, in which case you *will* be able to create an offscreen buffer that supports alpha to use to create your textures.

Hope this helps.