If you have 'Display Reciprocating Links First?' set to YES under your 'Link Preferences' section it will override the auto rotation of your links that are reciprocating. If you change the 'Display Reciprocating Links First?' to NO your links will automatically rotate properly.

Your links pages will rotate alphabetically, starting with A and going to Z every 24 hours. The rotation occurs daily at 12:00am, midnight, Eastern Standard Time. It is not currently possible to change the frequency or time of rotation of your links pages.