Is this a bug? When running the Near tool on a feature class (file geodatabase) whose table is joined to another, the Near tool fails (error 999999). Remove the join or export the feature joined feature class to a new feature class or shapefile and the tool works.
This has been logged to be reviewed as a bug. [#NIM076453 Near tool fails with Error 999999 when the input feature class used has a joined table. ] It is new so it cannot be searched on our support site yet. But the workaround would be to do what you did with exporting the data or the join can just be removed before running the near tool and reapplied after.
The main reason this is probably failing is because the Near tool is adding two new fields to the feature class. Because of the join, the table takes on altered field names that reference the table as well. It looks like the tool is not capable of recognizing that the join has modified the names in order for the new fields to be added properly.