Just double checked my invoice for my Win8 upgrade, the charge is handled by Arvato Digital Services, not Microsoft. Regardless of who the merchant is, it would not make sense that your Windows activation key be tied to your payment account. Yes, you bought Windows 8, they charge you and then give you the key but not "charge you upon activation". I would bet either Paypal or whoever is handling the merchant services for Microsoft accidentally charged you TWICE where the second charge coincided with the timing of your second activation.
@Welch, Windows 8 upgrade works pretty much the same as it was for Windows 7 upgrade. You can do a full clean install without prior versions installed or prior keys. To activate an upgrade (just like Windows 7), you need to change a reg key (bootmedia install = 0) and then cmd slmgr /rearm, activate, done.
And yes you can install Windows 8 without an internet connection. You just need to activate online. What are you rambling about? OP was asking about being charged twice for his purchase, not your emotional opinions on Windows 8. That discussion belongs somewhere else.