The "Command Shortcut" window that appears if the "When I press keys" option for a command is first checked, or the "..." button clicked had the "Use variable hotkey (Advanced)" option added; When this option is checked, the text within the key icons actually gets darker(I.E. they become less gray when grayed out).
What I assume to be the base color(anti-aliasing adds others) changes from #696969 to #555555.
The "clear" link also becomes visible when this occurs, even is it wasn't before(if no keys had been selected/pressed).
This was introduced with v1.7.2.26, when the feature was added.
I feel it would be clearer that the buttons are disabled, if the text becomes lighter gray instead, and if the "Press Key" button also swaps to the dark gray image state(which is already used if only modifier key(s) are selected).
Obviously this is a minor major issue, meaning it will not matter at all for hold up the next release, so it isn't that important must be fixed immediately.
EDIT: Buttons are now a darker color in v1.7.3.1, making it apparent they're disabled.
However, "Clear" still appears when "Variable Keypress (Advanced)" is checked, even if no keys were selected.
EDIT#2: "Clear" still appears in v1.7.5.8
EDIT#3: "Clear" still appears in v1.8.3.21
EDIT#4: "Clear" still appears in v1.8.3.22