The Fences icon sizes do change with the CTRL resize. However, the issue is present whether I use the CTRL method or simply select a predefined size, such as "classic icons." It only goes away when using large icons, as stated above.
Clean boot did not make a difference.
I obviously can't see the source code, but I suspect there is something unique about my system, perhaps the graphics card or something, where the column calculation is less than minimum snap size. So when I set it to a one column width, let's say that's 50 pixels. But the column calculation says a column is actually 48 pixels, so it incorrectly creates two columns.
If I could freely size the column below what it thinks is only a single column wide, I could work around the issue, but it does not let me.