What LW shows as junk is determined by your config of the junk filter. If you think too many good files are showing up as junk, you can change how strictly the filter operates...relax it more. You can also use the option to forget all training data...start from scratch again Tools > options > filters > junk will get you to the page.

Some people like the junk filter & some really hate it! See if this link helps...it's pretty long but has some good tips.
Junk Filter