Was there trouble with your RAF link originally? Things like upgrading a new account and then having Billing fix the link means that any levels and experience earned before the link is correctly applied aren't counted. Unfortunately, there is no way to go back and add those in as earned levels to grant.
Transferring a character to the recruit account means they only earn levels from the point they are on the recruit account. Similarly, starting a DK means they only earn levels from 55 up (on each even level attained, as I recall).