Check the Directory table and Shortcut table on the Tables tab in Setup Editor by right clicking anywhere in the tables tab and selecting Find Error. Errors in the tables are indicated in red.
In many cases the errors are due to unnecessary entries. If you determine that the entries are unnecessary to your installation, you can delete them removing the files from the Installation expert.
Although it is best practice to remove objects from the GUI, it is sometimes necessary to edit the table to remove the orphaned entry. To do this, right click on the files, and selecting "Delete Row(s)". After a row has been deleted, search for the primary key entry for the deleted row by selecting the tables tab and selecting Find in all tables to ensure that there were not other rows in the tables dependant on that row. These orphaned rows will also show up as red cells.