On Windows Vista Basic Home (and probably all Win versions) Using Three Column view, the columns selected do not display as set in View -> Set Displayed Columns. Other views, including Standard are ok. But in Three Column view only Subject and Size columns display (regardless of settings in Set Displayed Columns). Any user that prefers or needs Three Column view on Win will not be able to use this Claws for Win.
That's not a bug, that's by design. This is how '3 columns' view works, regardless of the OS. What you are right about though is that '/View/Set displayed columns' should not show columns that cannot be displayed in the current layout.
Can you even configure what to display and what not to display in Three Column layout? If not, perhaps the best solution would be simply to make the "View -> Set Displayed Columns -> in message list..." disabled while this layout is active.
I have three column view and the size column is disabled. So you can have little influence at least.