You are probably getting a blank column because you included no affiliations in the affiliation tab of the report set-up.
The affiliation code column in the user defined profile export is designed to contain a list of the affiliation codes attributed to the profile from the list of affiliation codes selected.  An example will make this clearer.
In the report selections you select the various fields you want to export and on the affiliation code tab you select affiliation codes for board members, committee members and donors.  When you run the export you get an question "Would you like to include the selected affiliations assigned to each of the profiles in your export?" and if you answer "Yes", an additional column of data at the end of the fields you selected will appear.  In this example, the affiliation code list will include board members, committee members and donors.  If a particular profile is also a Giving Circle Member, an attendee at a function or some other affiliation, even though they have those affiliation codes, they will not be listed.  Only the affiliation codes in the selection list will be included.
Thus, if you did not choose any affiliation codes on the affiliation code tab, there will be no codes to display.
The regular Export to Word Processing also includes an affiliation code column if requested, but this column will contain all the affiliation codes for the profile, not just the selected ones.
If you want to know which profiles have which codes from a group, you would use the User Defined Export.  If you want to know all of the affiliation codes for each profile, you would use the Export to Word Processing.
One use for this export option would be to select on two affiliation codes and see which profiles have only one of the codes, but not both.  Analysis on shared characteristics is another analysis you could perform.  Did everyone attending a particular event also give in a particular year ( assuming you have an affiliation code for annual giving)?  There are many ways this particular export can be valuable.