Try the following:
-Go to your MacintoshHD and open the folder "Library", then "Application Support", then "ProApps".
-Remove the File "ProAppsSystemID" to the Desktop, if it exist and restart Aperture.
Reenter your serial number, hopefully for the last time.
If this did not help:
Sometimes Aperture writes the "ProAppsSystemID" into the temporary directory "/tmp".
Check if you can find it there: Launch the "Terminal" application (from Applications > Utilities) and write into the Terminal window:
If you see "ProAppsSystemID" there, move it into the folder:
Your Macintosh HD > Library > Application Support > ProApps
I suggest calling Applecare:
Support and AppleCare
You can call 1-800-275-2273 within the US.
You might consider Repairing Disk Permissions on the hard drive using Disk Utlilities since it's occurring with multiple apps.