I just double-checked everything again, even correcting a couple minor issues in my billing information, but whenever I try to add Rebellion to my card, it always comes up at $39.95 (plus $2.40 for tax).
I've looked at my available downloads, and I have all 3 Sins games registered. The original that's listed as a Download + Retail (it's one of the last games I bought a boxed copy for), with Entrenchment and Diplomacy Download-Only. All have their respective keycode listed.
I only have the one e-mail address I've ever used for Stardock/Impulse.
Thought: Is it possible the discount isn't applied//reported until after I punch-in my payment info? I haven't progressed past that point since I've not seen the discount.