For me, only the top module (News and Analysis) disappears - the Tag Cloud is always visible. Have you looked at the viewing permissions for the News and Analysis module? Is it possible it is only set to show on certain pages/sections?
We are looking for a solution since several weeks ago now, and we really don't understand what's going wrong.
In our news section we have a left menu working very well, but it disappears when we read a post.
For example :
Left menu :
Left menu (news and analysis etc...) disappeared :
If someone can help us on this, we are close to open the web site officialy and we have only this "bug".
For now we are working with Tiki 6.1
Any ideas are welcome.