Here is where the confusion comes in. The EIJ, as anyone who has studied al Qaeda knows, is as much "al Qaeda" as Osama bin Laden himself ever was. A number of accounts have pointed out that the EIJ merged with al Qaeda in 1998 (or not fully until 2001, depending on who you talk to). The implication being that the EIJ wasn't really "al Qaeda" until that time. This is nonsense for a lot of reasons.
The EIJ and its leader, Ayman al Zawahiri, who is al Qaeda's #2, have worked closely with bin Laden since the mid-1980's. There is ample evidence of this close working relationship from then on. Montasser al-Zayyat, an Islamist attorney in Egypt who represented Zawahiri's terrorist colleagues in court, has explained this in his book The Road to al-Qaeda. Zayyat writes: "Zawahiri managed to introduce drastic changes to Osama bin Laden's philiosophy after they first met in Afghanistan in the middle of 1986, mainly because of the friendship that developed between them.