It's normal for the pedal to sink about 1/2" when the engine starts and the booster gets vacuum. I can't explain why but know it happens (see Bentley 520-5, Booster Quick Check). There's a lot more system pressure than you can apply at the pedal.
I think the problem is in the bleeding. Give us some details.
When everything is new, I think it helps to apply full pedal pressure occasionally during each piston's bleed cycle to take up all the rotor-pad-grease-shim-piston clearances. If you don't do it, the booster will — accumulating a bit more pedal travel at each of the 6 pistons.
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Bruce Young, '93 940-NA (current), 240s (one V8), 140s, 122s, since '63.
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