Are you using the latest version? Not sure what a red line would indicate, but it might mean a missing master. If you have FO3Edit then run that and when it asks which plugins to use just click OK, this will load all the ones that are active in your FO3 installation. Then watch the message pane to see if it mentions any errors such as missing masters.
Yes, using the latest version - just got it last night. I have run FO3Edit and nothing stands out there. I have run the game once or twice and the mods that are marked red seem to be working. Fingers crossed I haven't broken something that bites me later!