I first encountered this problem in early 2010 whilst using LW 4.16. Even same issue with an alternative startup drive.
I found the same problem with every LW 4 version, FrostWire 4 and the LW 4 clones such as MP3 Rocket.

Symptom:

ie: under the LimeWire menu on the apple toolbar, there was no longer any Preferences option.

The only way to access the preferences I found was by going to the Library window and choosing configure shares. This was a backdoor approach. (Perhaps due to sharing lots of files but I found the changes to settings did not always stick after a restart 100% of the time.)

An alternative fix:

Only a few weeks ago I discovered an alternative approach. Install any of the LW 4 skins and you will be able to access the preferences options via the approach Windows users do. ie: once you have changed to another skin, find the Tools menu on the actual LW program. Then choose options and there you have it.

Someone recently mentioned to me they had the same problem. So this should be a good fix for you. Besides, you have many skins to choose from if you use my recently compiled Skins installer with 100 skins options.

I created a Skins installer for OSX users for each of LimeWire 4 and FrostWire 4. If you do decide to use the skins installer, try out my skin lol LOTR Ult.

4 locations you can download the Skins installer for LimeWire 4: . LimeWire and FrostWire OSX Skins - Mediafire, . . . LimeWire Skins OSX - FileCloud,

LimeWire Skins OSX - 4Shared, . . . LimeWire Skins OSX - Hotfile.

FrostWire: . FrostWire Skins OSX - FileCloud, . . . FrostWire Skins OSX - 4Shared . and the above MediaFire link.