Try the following -
Disconnect all peripherals from your computer.
Boot from your install disc & run Repair Disk from the utility menu. To use the Install Mac OS X disc, insert the disc, and restart your computer while holding down the C key as it starts up.
Select your language.
Once on the desktop, select Utility in the menu bar.
Select Disk Utility.
Select the disk or volume in the list of disks and volumes, and then click First Aid.
Click Repair Disk.
Restart your computer when done.
Repair permissions after you reach the desktop-http://support.apple.com/kb/HT2963 and restart your computer. After reaching your desktop try the Keychain Preferences again.
If you are still having issues after doing the above, try the following and post back your results -
Use Spotlight to search for a file called login.keychain.
Users/YourUserName/Library(which is a hidden folder and won't show in Finder)/Keychains.
Click Go in the menu bar then Go to Folder and type in /Users/YourUserName/Library and hit the enter key.
Look down the list of folder and find Keychains. The "login.keychain" file should be inside.
Open /Applications/Utilities/, CONTROL-click on Keychain Access->Show Package Contents->drill down to /Contents/Resources/, and double-click on Keychain.menu. Does that put it on the menubar? If so, see if it works and see if the preferences are now working. Alternatively, quit KA, move this from your user/s /Library/Preferences/ to the Desktop, relaunch KA, reset the prefs, and see if that fixes things.