AutoTrack problems are really difficult to help with unless we can see the database, look at the link cards, the restrictions and rules, clocks and assignment grids etc.
So first things that spring to mind are:
in the clocks check that you have the Link category selected in the clock position not the specific link card number.
(depending on the version of AutoTrack) Goto> Reports&Statistics>More Reports (including Copyright)>Songs/Links>items Not Scheduling then select the relevant link Category. Run the report and see if it tells you anything useful.
Broadcast Radio Ltd