@bobbyD Using RM5.1, copy/pasting a "Simple Conditional" within the rule OR importing/pasting the clipboard from another rule does not update the "Manage Conditions" list.
When I imported and pasted from another rule, then started to try to recreate/delete the lines associated with the missing conditions, suddenly ALL of the conditions showed they were "unused". The rule appears hopelessly corrupted now.
What happens when you click on one of the Conditions? The (unused) thing is a UI artifact, and is not necessarily indicative of a problem. Have you gone back to the main page of the rule, and then back in to Actions?