This typically happens if you copy the game to another machine or reinstall windows with an existing install of the game already present.

In any case, if you delete the .bin files from C:\Documents and Settings\All Users\Application Data\Ironclad Games\Sins of a Solar Empire\License (location should be similar on Vista under C:\Users), you should be prompted for your serial key and email upon attempting to run the game again, at which point it will rebuild the bin files and should be ok.