Lena,Are you actually using jD Custom Fields? If not then no problem.
If Config - 'Custom Data Fields' title entries, those on the lefthand side, are blank then you are not using jD Custom Fields.
If you are using them then you would have needed to edit one of the Files or Downloads Details Layouts - see articlehttp://www.jdownloads.net/documentation-for-jd3-2/general-items-v3-2/using-custom-fields
If you have done all of the above then the jD Custom values will appear on every Download whilst using the relevant layout. With the jD Custom Fields then the titles appear on all Downloads - this does not need to happen with Joomla! Fields.
If you are using jD3.2 Cusom Fields have you set any defaults? They are on the right hand side in the Cofig - 'Custom Data Fields'.
If yes then you can set defaults in the Joomla! Fields and they will appear in every Download where you have followed the setup complete with a modified layout or layouts as described in the following articlehttp://www.jdownloads.net/documentation-for-v3-9-beta/general-items-v3-9/converting-jd-custom-fields-to-joomla-fields
Hope this helps but please let us know what you have setup