I'll explain one context in which it continues to happen in the hope that that might shed some light on what I'm doing wrong.
When I open up a new, blank canvas, I can render the gradient just fine.
When I enter text on the new, blank canvas, I can also render the gradient.
When I select around the text (via Shift+magic wand) and delete the area, I can also render the gradient (though it covers over the text).
Once, however, I have selected around the text (via Shift+magic wand) and the inverted the selection (Ctrl+I), then the gradient tool no longer works, giving those nubs only.
In case it's relevant, I am trying to creat a tricolor gradient text.
Note: Rebooting Paint.Net seems to fix the problem. I was just hoping I could find another means of remedying the problem without having to close out of the program each time.