From the FAQ page

To correct the problem, do the following:
* Start Ad-Watch, if it is not already running.
* Right-click on the Ad-Watch icon in the system tray (in the lower right corner by default) and then select "Ad-Watch Settings".
* At the bottom of the Ad-Watch window is an item labeled “Automatic�. Click on it to turn it into a red cross, i.e., turn off “Automatic�.
* Start Ad-Aware SE and click on the “Ad-Aware Configuration Window� icon.
* Click on “Startup� and make a change -- any change will do -- and click on “Proceed�. This will cause Ad-Watch to issue an alert notifying you of the change. Accept the change. In Ad-Aware SE set the startup options you want use.
* To prevent Ad-Aware SE from starting at boot time, under "Startup Scan Mode" select "No automated scanning".
* Make sure that the items under "Startup Action" and "Automatic Updating" have a red cross next to them, then click “Proceed�. Ad-Watch will again pop up an alert notifying you of the change.
* Accept the change. Ad-Watch will now accept the registry update and Ad-Aware SE will be configured not to start at boot time.
* At the bottom of the Ad-Watch window, turn on “Automatic�. The changes to the settings you made will now be accepted by both Ad-Watch and Ad-Aware SE.
* If you are running any other registry protection tools, you will need to accept their alerts as well during this process.