Does it keep popping up after you've closed it, or is it only the once on startup?

If it's only the once, try deleting LW's preferences folder when LW's properly closed. See points 2 & 3 below for instructions
Fixes for LimeWire
If you've used older versions of LW before, you could have a preferences folder in the location mentioned on point 2, or as mentioned in point 3...so check for both. Remember to show hidden files & folders. After deleting that folder, you'll have to go back through your options & reset everything to the way you had it.