Issue: Doing a Spacial Join or Selection returns all items.
Description:
If you join a layer to a table you may be unable to use that layer in a spacial join to another layer. When using a layer with joins in ArcMap 9.3 you might encounter the issue where all the items in a layer are selected instead of the selection based on your criteria.
Solution:
The solution is to export the layer with the join to a separate layer file, then use that layer to do the spacial join/selection.
Pee Dee GIS Users Group 
April 27, 2010 at 9:17 am
If your join happens to be to a access table you will need to first convert to an excel, or other file. For some reason when you export a layer joined to an access table the data goes away not sure why this happens. But the easy work around is use excel for your joins.