Shame you didn't post your SQL, you can try something like this in your Make Table Query.
To see how this works create 2 Tables, Table1 and Table2 add to both an Auto Number Field and name both AutoNumberField . In Table1 also add 2 Fields and name them Field1 and Field2.
Paste this SQL into a new Query, Run the query. You should now have a new Table Table3 with both Auto Number Fields named AutoNumberField1 and AutoNumberField2.
SELECT [Table1].[AutoNumberField]+0 AS AutoNumberField1, [Table2].[AutoNumberField]+0 AS AutoNumberField2, Table1.Field1, Table1.Field2 INTO Table3
FROM Table1 INNER JOIN Table2 ON Table1.AutoNumberField = Table2.AutoNumberField;
Table2.AutoNumberField;
Now open the new Query in Design View and follow the method I've used in your own query.
Hope this makes sense.
Bill