Try this:
1. Quit QS
2. Move the folder ~/Library/Application Support/Quicksilver to your
desktop. (For those who don't know, "~" is the Unix (Mac OS X, Linux,
etc.) shorthand for your user folder.
3. Restart Quicksilver. You should now have a vanilla default setup.
4. Check to see if your trigger window is behaving itself now. If so,
add your triggers.
5. If there is any data you need to restore from the old settings, you
can drag the necessary files from the old Quicksilver folder on your
desktop into the new one that will have been automatically created in
the same place that the old one used to be. However, I recommend that
you start afresh by re-downloading your plugins and re-adding items to
your catalogue using the QS preference panel.