You're not adding "a Continuous Section Break at the end of the second
column"; you're adding a Continuous section break at the end of the
two-column section. The default behavior of Word in this case is to balance
the columns. If you don't want them balanced, there is a Compatibility
setting (Tools | Options | Compatibility) that you can set to change this.
You can also insert column breaks or use paragraph formatting ("Keep with
next," "Keep lines together") to force Word to break the columns where you
choose.

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Suzanne S. Barnhill
Microsoft MVP (Word)