Surprise! There's a bug in Netscape Navigator 3.0.x.
Yes, there's a bug in versions 3.0 and 3.0.1 of Netscape Navigator that sometimes causes Navigator to forget what protocols have been registered by Seeker (and other similar utilities - for more information on protocols, read the Frequently Asked Questions chapter in the Seeker 1.0 Documentaion).
Fortunately there are two fairly simple work-arounds for this problem. The first is that you can launch Seeker each time you want to perform a search instead of allowing Navigator to automatically launch Seeker for you.
The second work-around is to install the Netscape Navigator preferences file included with Seeker (found in the accompanying "For Navigator 3.0.x Users" folder). You can do this by placing a copy of the included Netscape Preferences file in the "Netscape ƒ" folder that's found in the Preferences folder of the System Folder of your startup disk.
The only drawback to this work-around is that you'll need to reconfigure your favorite settings (be sure to quit Navigator before installing the new Netscape Preferences).