Make sure that Shapefile2 is going into the LEFT side and Shapefile1 is going into the RIGHT side. Before the FeatureJoiner remove all the attributes from Shapefile1 that you don't want to be joined (Make sure that you still have the attribute which you want to use to do the join though).
In the output writer/feature type for Shapefile2, be sure that the schema definition is set to Automatic (not manual).
Note: be sure to output to a new location so you don't overwrite the original in case anything goes wrong