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When enabling blend you need to specify the blending function otherwise it will default to the last one used which may not be desireable(which is what is happening in you case). Additionally it is better to set the GL states once before rendering everything and not everytime you need to render every quad. GlStateManager.pushMatrix(); GlStateManager.translate(0, 0, 0); Why? Why are you translating by 0,0,0? It does absolutely nothing. You do not need matrix interactions here at all.

You probably want blending not alpha testing. (Haven’t looked at your code, going off the title) Also, DONT use GL directly (GL11.glColor) use GLStateManager

The problem here is that the rest of the game uses GLStateManager to change GL states and GLStateManager has it's own copy of each state value. Thus if you change a value through OpenGL's direct API the state manager and thus the rest of the game won't know about it and still think the old one is used.