Using the IMGT/GENE-DB service to find RSS
I'm not clear what "Locus", "Main locus", and "IGMT group" mean here
  exactly. Specifically, what is the difference between "Locus" and
  "Main locus"?


From the same site:


  A locus is a set of IG or TR genes that are ordered and are localized
  in a same chromosomal location, in a given species. […] 
   A locus comprises the genes of different groups which participate
  potentially to the synthesis of a polypeptide of the same 'chain
  type'.


Main locus should have been Locus minus the orphons:


  A chromosomal orphon set is a set of IG or TR orphons (genes outside
  from the main loci) belonging to a same group and localized on the
  same chromosome in a given species.



However the Main Locus and Locus have the same options; Options for the Locus should have been chromosomes. They must have made a revision in the site but forgot to change the help. I tried setting all the options except any in Locus and selecting all for the Orphons; it yields no result. It works only if you set any in Locus. So it seems Locus option is useless; you can set the Locus as any by default.
 For confirmation it is best to ask the authors.

From the changelog:


  16 April 2012
  
  
  Update of the IMGT/GENE-DB Query page:
  
  The search criteria are organized according to the axioms IDENTIFICATION, LOCALIZATION and CLASSIFICATION of IMGT-ONTOLOGY.
  Addition of new search criteria:
  
  
  MolecularComponent (IDENTIFICATION)
  Locus (LOCALIZATION): includes main loci and chromosomal orphon sets
  Main locus: "all" value allows to search genes of all main loci.
  Chromosomal orphon set: "all" value allows to search genes of all chromosomal orphon sets
  
  


For details on the IMGT classification you should refer to this paper. 

Fixing a Locus option does not change the IMGT dropdown box option but the results are different. If you try your example and set Main Locus as IGH and IMGT Group as IGKJ you would get no results. It is just a problem of the web interface. Apparently the search works fine.



Running the search

I searched with the exact same criterion as you mentioned and did not get any sequences smaller than 38nt. There must have been some bug which seems to be fixed.