I did some further investigation after seeing the same problem in Blender.
There are at least two ways in Gnome to remap Caps Lock to a Ctrl key:
1:
Keyboard & Mouse
Additional Layout Options
Caps Lock behavior
Make Caps Lock and additional Ctrl
2:
Keyboard & Mouse
Additional Layout Options
Ctrl position
Caps Lock as Ctrl
Turns out that these are different under the hood, and when I stopped
using #1 and started using #2 (Caps Lock as Ctrl), all applications
now behave as expected, respecting my choice.
This bug can probably be closed, but could serve as a "warning" of
sorts to anyone else having the same problem.
