I just bought the game yesterday and now it will not let me register it since it says that my number is not a valid one or that it does not match the email address that I supplied to Stardock and SoaSE.
If you bought it online direct, you shouldn't need to register it. If you used a different email address on the store as you use on forums/SDC though, that could cause the issue you're having. You'll want to contact
[email protected] and request an account merge in that case.
As to the numbers themselves being different, that is completely normal. They should both be valid and treated as identical by the system.