I did discover some workarounds.

1. In the sample app I provided, I have since added an event handler for the form's Shown event.  Here I call Refresh() and PerformLayout() on the flow panel.  This causes each checkbox to paint itself and then redo its layout, at which point it resizes correctly.  It appears that something in the painting of the control causes it to update the info it needs to resize itself correctly the next time it does a layout.
2. However, this only works for checkboxes that are currently displayed.  In our actual app, the flow layout panel is inside a larger scrollable container, and some of the checkboxes are initially off screen.  Since they aren't displayed, calling Refresh() on either the panel or on the checkbox itself doesn't make a difference.  Instead, I had to hook into the Paint event of each checkbox and call PerformLayout on the checkbox at that time.  This significantly slows down the process of painting checkboxes when they initially scroll into view since the containing panel has to redo its layout every time a checkbox resizes itself.

Attached is a sample app.

We're using 17.1.