That should not happen, provided that you Save your Project. Now, the Columns setting is Project specific, and NOT global. Hence, if you are working on 3 Projects, you must manually set the Columns for each and Save. Open another Project (new, or old) and you get the default Columns. If your installation is loosing Columns setup, after a Save, something is wrong.
IIRC, Columns is a global setting in CS4, but do not have it, so I am going from my memory of others' posts.