If secure input is active, BTT can not differentiate between left and right modifier keys. In that case the shortcuts you defined will work with both left and right modifiers. Because of this they might block existing shortcuts.
If it says secure input was activated by loginwindow, this is usually not true. Most of the time some app activated secure input (e.g. in a password field) and forgot to deactivate it. There are usually two ways to solve this: quit all apps one by one to find the culprit or logout of macOS and back in.