What about on your external drive ?
Sorry, I actually am assuming that you have checked there, but...
Hey, you never know...

Checked all drives and the two files are missing. Does this mean that LW can only hash and memorise up to a certain size of total files? This is an important issue for the future as I can't imagine I am the only person slowly ripping all their music partly as backup, partly because I'm anally retentive but mainly to allow me to access via my iPod. It also allows me to set up playlists that can be set to play for hours through my home on iTunes. These are the primary reasons for ripping but once done then I'm happy to share. I would imagine this would be the same for many people. My total collection will be less than 100gb but then I will start on vinyl which may add a few more gbs! LW will need to take this development into account in the future - not just because of me as I have no relevance at all but I would guess I'm not alone in doing this.

The two files are in the LimeWire Folder inside the Preferences Folder inside the Library Folder of your home directory. Make sure these folders are writeable by you. I have occasionally seen these folders owned by root or similar bad things, this could prevent LimeWire from storing these files on shutdown.

I've checked and these files are missing.

Does it look similar to this:

jum@ra dist$ ls -la ~/Library/Preferences/LimeWire/
total 448
drwxr-xr-x 21 jum staff 714 16 Mar 12:43 ./
drwx------ 245 jum staff 8330 16 Mar 12:43 ../
-rw-r--r-- 1 jum staff 6148 22 Jan 02:47 .DS_Store
-rw-r--r-- 1 jum staff 102 16 Mar 12:42 Cookies.dat
-rw-r--r-- 1 jum staff 108 15 Mar 16:48 Display.props
-rw-r--r-- 1 jum wheel 3703 11 Mar 00:49 LimeWire.bsh
drwxr-xr-x 3 jum staff 102 8 Feb 2003 META-INF/
-rw-r--r-- 1 jum staff 276 10 Mar 14:57 bugs.data
-rw-r--r-- 1 jum staff 58900 16 Mar 12:43 createtimes.cache
-rw-r--r-- 1 jum staff 158796 16 Mar 12:42 fileurns.bak
-rw-r--r-- 1 jum staff 158796 16 Mar 12:43 fileurns.cache
-rw-r--r-- 1 jum staff 113 16 Mar 12:42 filters.props
-rw-r--r-- 1 jum staff 22965 16 Mar 12:42 gnutella.net
-rw-r--r-- 1 jum staff 201 16 Mar 12:42 installation.props
-rw-r--r-- 1 jum staff 1291 16 Mar 12:42 limewire.props
-rw-r--r-- 1 jum staff 1030 10 Mar 2003 public.key
-rw-r--r-- 1 jum staff 181 16 Mar 10:00 questions.props
-rw-r--r-- 1 jum staff 1693 16 Mar 12:42 tables.props
drwxr-xr-x 22 jum staff 748 3 Feb 00:14 themes/
-rw-r--r-- 1 jum staff 421 11 Mar 00:37 update.xml
drwxr-xr-x 6 jum staff 204 10 Mar 2003 xml/
jum@ra dist$

Thanks jum--so that's how you get that info!

Open Terminal (in the Utilities folder)
Type "ls -la ~/Library/Preferences/LimeWire/" into the terminal window and hit return.

Correct?

-rw-r--r-- 1 stief staff 201631 Mar 3 16:40 fileurns.bak
-rw-r--r-- 1 stief staff 202420 Mar 15 07:25 fileurns.cache

[I--so that's why my fileurns.bak hasn't changed its date modified! I've been using the official build on this computer, and your CVS build on the other.]

Yep, this how to get that info on a Unix shell. And yes, the official version does not know about this filurns.bak thing.

Please remember I am using a Mac so I don't normally need to understand how it works - it just works.
In prefs I have
MANIFEST.MF
limewirePro_theme.lwtp
limewirePro_theme
windows_theme.lwtp
windows_theme
default_osx_theme
default_osx_theme.lwtp
default_theme.lwtp
default_theme
black_theme
black_theme.lwtp
xml
update.xml
themes
tables.props
questions.props
public.key
META-INF
limewire.props
installation.props
gnutella.net
fileurns.cache
Display.props
createtimes.cache
bugs.data
Cookies.dat

Does this make sense? Would it be easier if I just uninstalled and reinstalled? If so how do I do this on the Mac? I usually drag and drop into the trash.

I feel I am getting out of my depth here!

So you have a fileurns.cache there! Did LimeWire indeed do hash all files to the end before you did quit it?

Yes... above he mentions that he ran the full files through to a completion of hashing.