Blender, the open source 3D modeling tool, wasn't behaving as expected when manually adding vertices. It turns out that one of the preferences I had set in Ubuntu was the problem.

In Blender you can add vertices by selecting an existing vertex, holding down the control key and left clicking (a.k.a. Ctrl-LMB) on the location where you want the new vertex added. I was more than a bit surprised when this wasn't working for me... it used to work, after all. Then I remembered that a while back I had enabled locate pointer in mouse preferences. The solution was to disable this setting (the highlighted item in this screenshot):

Once changed back to the default setting, Blender now works as expected.