Cannot populate all fields using spatial join script tool

I am trying to create a script tool that spatially joins point and polygon features so that they create a new feature class with only user specified fields included. I have created a parameter that allows the user to check off which fields they want to include, but if both input and target feature classes have the same field name in their table, only one of the fields will be populated in the output table (ie. both have NAME field). If I use the spatial join tool the new table will include populated NAME and NAME_1 fields, but not in a script. I have also tried to check the 'maintain fully qualified fieldnames' in environments so that each field name is unique, but this doesn't seem to help. If anyone has any idea it would be greatly appreciated. Thanks

Jesse