Alpha Add blending mode! AE's default transparency blending is not linear. hence at 50%/50% the actual transparency is more like 80%, not 100%.
As mylenium said, switch to alpha add blend mode.
So now you might wonder why 50+50 doesn't equal 100. It's because opacity, in real world, don't work this way. If you take a thin sheet of paper and tape it on your window, you'll see that light is coming through. This thin paper is about 50% opaque. Now if you tape a second sheet on top of it, you'll see that light is still comming thru. It's because the first sheet filters 50% of the incomming light, and the second sheet filters 50% of the 50% incomming light.
50% of 50% still leaves 25% light, and a third sheet would let 12.5% and so on and so on. And AE calculates it's opacity exactly like that. And as it's sometimes not conveniant (like in a cross dissolve) they added the alpha add, where 50%+50% = 100%.
Thank you, Mylenium, that works great. I strongly suspected the answer lay in the layer modes.