Are you using Vista?? If you are, check out these threads about files not showing.
Files missing from libary Can't find files outside LW
If you're using LW 4.16 with XP, have a look for your recently downloaded files in C:\Documents and Settings\your username\Limewire Saved ...are the new downloads there? Or look in C:\Documents and Settings\your username\Shared.
Or use your computer's search to look for some of the file names...do they show up anywhere?