I don't know how it is for you guys, but I had the steam version installed first, and then, when the 1.5 update came, I manually installed the 1.43 from taleworlds site. This new version automatically registered with the same CD-Key as the steam version, I didn't even get a popup once, it was unlocked right from the start. This wasn't a problem for me, of course, because I only have 1 CD-Key anyway, and just wanted cRPG to work again.
Maybe you have the same behaviour? I'm not sure if it's even possible to use two different CD-Keys on the same computer...