sorry for the very very delayed reply. i was thinking 'wondering why' was helping you.
anyway, have you uninstalled everything including the java? you have deleted limewire, right? try uninstalling java as well. after you've done that there should'nt be anything popping or at least giving a hint that you have limewire in your computer.
uninstall it first then let me know what happens. but i do hope you already have it fixed.