UPDATE: iTerm version 0.9.5.0821 has been released which is intended to fix this. I haven't tested it.
I just upgraded to iTerm version 0.9.5.0820 from 0.9.5.0611 on Mac OS X Leopard, and found that iTerm had forgotten or lost all of my preferences and bookmarks.
I fixed it by;
~/Library/Preferences/
net.sourceforge.iTerm.plist
to net.sourceforge.iTerm.plist~
iTerm.plist
to net.sourceforge.iTerm.plist