The iLok works for all applications and plug-ins for which it carries a license, but these licenses are not transferred automatically to the dongle. In fact, when you buy it, the dongle is empty. So, first you have to buy the licenses, and then transfer them to the dongle. In the case of a Melodyne license, proceed as follows:-

First you have to purchase the iLok option from the Celemony Web Shop (except for Melodyne plugin, which already comes with an integrated iLok option). Next you open a user account at the myCelemony page and follow the instructions under "Transfer iLok license". A license will then be sent to ilok.com from which you can download it onto your dongle. The procedure is very simple and you can use any computer connected to the Internet for the purpose.
Transferring the Melodyne license to the iLok dongle

Also make sure you are using the latest version of the iLok software — i.e. the driver provided by the manufacturer, PACE, which you can download from the PACE site www.paceap.com Select Download Drivers from the list box in the END USERS pane at the top and commence the download from the window that appears.