Well, since there are multiple users with the problem, and nothing looks out of place with the permissions on loginwindow.plist for anyone, I don't know what the cause is (we'd need to bring the coders in to figure that out). But there are a couple of workarounds I can suggest in the meantime.
Option 1: Create a service to launch Quicksilver
Open Automator, and select the option to create a new service. At the top, set it to receive no input. In the sidebar search box, type "Run Shell Script" to locate the Run Shell Script Automator action. Drag this action into the main workflow area. Change the content of the shell script to read the following:
if [[ $(killall -s Quicksilver 2>/dev/null) != "" ]]
then
open -b com.blacktree.Quicksilver
else
open -b com.blacktree.Quicksilver
open -b com.blacktree.Quicksilver
fi
Save the service as "Open Quicksilver". Now, click on the application menu (i.e. the one called "Automator" when Automator is the front application), select the Services menu item, and then click on the Services Preferences... menu item. In the window that opens, find your Open Quicksilver service and
assign it the same keyboard shortcut that you use to activate Quicksilver when it is running. For example, if you use ⌃Space to activate Quicksilver, assign ⌃Space to this service (note: you may have to temporarily quit Quicksilver in order to enter the keyboard shortcut into the window). Tada! Now, whenever Quicksilver isn't running, you can press the same keyboard shortcut that you always do and it will start on demand for you. If Quicksilver is already running, it will catch the key-press itself before it ever filters down to the service.
Here is a picture of what the Automator window should look like when you create the service:

Option 2: Create a launch agent to kickstart Quicksilver when you login
Open Terminal and enter the following two commands:
mkdir -p ~/Library/LaunchAgents
nano ~/Library/LaunchAgents/launchQuicksilverAtLogin.plist
This will open an editor window within Terminal. Paste in the following text:
<?xml version="1.0" encoding="UTF-8"?>
<plist version="1.0">
<dict>
<key>Label</key>
<string>launchQuicksilverAtLogin</string>
<key>ProgramArguments</key>
<array>
<string>open</string>
<string>-b</string>
<string>com.blacktree.Quicksilver</string>
</array>
<key>RunAtLoad</key>
<true/>
</dict>
</plist>
Press ⌃O to save the file (answering Y for yes when it prompts you to confirm), and then ⌃X to exit the editor. Next time you log in, Quicksilver should start. You should probably disable the Start at Login option in Quicksilver's own preferences.