UPDATE****: This tutorial has proven ineffective due to some corrupt BSD installations. We are therefore recommending that you use the iLiberty+ payload that XianLi has created. Read this for more information.
This tutorial only fixes issues with the 3.1 Installer version. Before attempting this fix please ensure you have updated your community sources and you have enough free space on your iPhone root filesystem. Also, if your installer is working fine please do not install this.
If you haven't already added iClarified to your Installer Source then follow this tutorial.
Press to launch Installer from your SpringBoard.
Press to select iClarified from the list of Categories
Press to select Installer Fix (3.1) from the list of Packages
Press the Install button at the top right of the screen.
Press the large red Install button that appears.
You will be asked to confirm installation. Click the large OK button.
When the installation is complete you will be notified. Click the large OK button.
You will be returned to the Categories list. Press and hold the Home button until you see the SpringBoard. You can now relaunch Installer and hopefully your issues will be resolved.
For further discussion on this method and other possible fixes please see this hackint0sh thread.
THANKS*: Thanks to XianLi for posting this method.