The junk filter does not filter out anything unless you train it to filter out certain things. If you select the wrong ones to filter out then it will not work well later. You can untrain it by going to LW's menu bar, Tools>Options>Filters>Junk Filter ...
Be sure what you add to the filter is actually junk! It is a dynamic learning filter so if you train it the wrong way it will make mistakes. Just be sure what you add to the filter "is" actually junk / spam.