Each time you upgrade WP you have to visit the My Link Order page where you do the ordering. In it’s current form the plugin has to patch a core file to make everything play nice with the built in functions.
The new version of the plugin I want to create will start fresh and not rely on these core files. I also want to switch to the new Widget API that is only supported by 2.8 and above. That will make life a lot easier for everyone.
Until I have that new version released I’ll make sure that the plugin isn’t completely broken by a new version, but there will be a point when I’m going to cut off any fixes and those on 2.8 will want to migrate to the new plugin. I’ve published this plugin for almost 3 years and it really hasn’t changed at all and is becoming a pain to maintain.