This happened to me too but not a major issue. I believe the new LW 4.12.3 is supposed to stop that from happening: http://www.limewire.com/english/content/download.shtml

Try fix the situation in the meantime, try deleting your LW Preferences folder whilst LW is closed; instructions here: Point #2 & 3 in Fixes for Limewire (sample image included at bottom of page.) But you'll need to re-set your LW options next time you open it.