When your search results are displayed, have a look to the left side of the results. You'll see different categories, depending on what type of search you've done...media, artist, genre, album etc. If you select 'All', you should see all the available results (& so the numbers you see in parenthesis will change). Selecting different options within these categories will change the amount of results shown, compared to the total results found.

However, if your junk filter has recognised some of the files as junk & if you've chosen (within LW's options) to not display junk...those results won't be shown

Has this started happening since you updated your Java? Some people have had trouble with Java 1.6.0_01. If it's a new problem, you could try installing this older version of Java & see if anything changes. Use the JRE offline installer & remove your current Java before you install this one.
Archive: Download Java 2 Platform Standard Edition (J2SE) 5.0 Update 11