I don't know exactly what is wrong, but it could be that you have a continuous section break immediately under the 2-section column. I think Word has difficulty trying to "balance the column length" in this situation.
If you click the Show/Hide button (the "Pilcrow" button to the left of the Zoom dropdown in the Standard menu) the section breaks should become visible and it may be easier to see what is going on. I would consider putting a next page section break at the bottom
of my two-column section, then enter the text in the 2-column section, then insert a continuous break (if that's what's needed) when you're done.
Peter Jamieson