I deleted the old ~/.lazarus directory and uninstalled Lazarus and FPC. I then installed Lazarus 1.6 with FPC 3.0. When I rebuilt the IDE to install some components, it completed the rebuild and restarted properly. However, when I closed it down and tried to restart it again it displayed the "Configure Lazarus IDE" dialog with the message "Warning: directory lcl not found". The component palette was empty apart from my custom components.
I found the solution in the "IDE options" dialog. In the "Files" section, the item "Lazarus directory" was empty. I entered "/usr/share/lazarus/1.6/", and after this Lazarus started up properly. So I suppose this is a small bug but easily fixed.
[Edit] Sorry, I failed to say that this is a 64 bit Debian Linux system.