Is your Aperture version a full Aperture 3 version or an Upgrade from Aperture 2?
If it is an upgrade, you need to enter the Aperture 2 (or 1) serial number as well.
If i is the full Aperture 3 version, check, if you entered the serial number correctly - some letters can easily be confused, 1, l and I, or O and 0.
And don't enter the numbers from the numeric part of the keyboard.
See this support article:
If you cannot find your Aperture 2 serial number, or cannot make Aperture accept your Aperture 3 serial, contact Apple, see Pro Application Replacement Serial Numbers