Hi and welcome to the forums!
The Construction Set sometimes behaves in unexpected ways, and this makes it very easy to make unwanted changes to the game. This is especially true for the faction, race, class, birthsign, dialog, area, and region windows, and I think this is what might have happened to your mod as well.
Unfortunately these unwanted changes often cannot be undone with the Construction Set and so you need to use third party programs to keep your plugin "clean" of changes that you did not intend to make.
The http://www.elricm.com/nuke/html/modules.php?op=modload&name=Downloads&file=index&req=viewdownloaddetails&lid=96 is a good tool for keeping your mods clean, and it's fairly intuitive to use. I'd advise you to open your plugin with it, and try to look over the different entries inside to figure out which ones don't belong there.
And remember to backup your mod often.