The easiest way to illustrate the problem is to run the following code (this code is contained in IndexSuperFile1.ECL) that uses two of the sub-files from the Creating and Maintaining SuperFiles article.

IMPORT $;

OUTPUT($.DeclareData.ds1);
OUTPUT($.DeclareData.ds2);

You will notice that the RecPos values returned for both of these datasets are exactly the same (0, 89, 178 ... ), which is to be expected since they both have the same fixed-length RECORD structure. The problem lies in using that field when building separate INDEXes for the two datasets. It works perfectly as separate INDEXes into separate DATASETs.

For example, you can use this code to build and test the separate INDEXes (contained in IndexSuperFile2.ECL):

IMPORT $;

Bld := PARALLEL(BUILDINDEX($.DeclareData.i1,OVERWRITE),BUILDINDEX($.DeclareData.i2,OVERWRITE));

F1 := FETCH($.DeclareData.ds1,
            $.DeclareData.i1(personid=$.DeclareData.ds1[1].personid),
            RIGHT.RecPos);
F2 := FETCH($.DeclareData.ds2,
            $.DeclareData.i2(personid=$.DeclareData.ds2[1].personid),
            RIGHT.RecPos);

Get := PARALLEL(OUTPUT(F1),OUTPUT(F2));
SEQUENTIAL(Bld,Get);

As you can see, two different records are returned by the two FETCH operations. However, when you create a SuperFile and a SuperKey and then try using them to do the same two FETCHes again, they both return the same record, as shown by this code (contained in IndexSuperFile3.ECL):

IMPORT $;
IMPORT Std;

BldSF := SEQUENTIAL(
  Std.File.CreateSuperFile($.DeclareData.SFname),
  Std.File.CreateSuperFile($.DeclareData.SKname),
  Std.File.StartSuperFileTransaction(),
  Std.File.AddSuperFile($.DeclareData.SFname,$.DeclareData.SubFile1),
  Std.File.AddSuperFile($.DeclareData.SFname,$.DeclareData.SubFile2),
  Std.File.AddSuperFile($.DeclareData.SKname,$.DeclareData.i1name),
  Std.File.AddSuperFile($.DeclareData.SKname,$.DeclareData.i2name),
  Std.File.FinishSuperFileTransaction());

F1  := FETCH($.DeclareData.sf1,
             $.DeclareData.sk1(personid=$.DeclareData.ds1[1].personid),
             RIGHT.RecPos);
F2  := FETCH($.DeclareData.sf1,
             $.DeclareData.sk1(personid=$.DeclareData.ds2[1].personid),
             RIGHT.RecPos);
Get := PARALLEL(OUTPUT(F1),OUTPUT(F2));
SEQUENTIAL(BldSF,Get);

Once you combine the DATASETS into a SuperFile and combine the INDEXes into a SuperKey, you then have multiple entries in the SuperKey, with different key field values, that all point to the same physical record in the SuperFile, because the record pointer values are the same.