Two problems here:

 Problem 1:

 While constructing the join columns list the optimizer does as follows:
  1. Sets the join_using_fields/natural_join members of the right JOIN 
   operand.
  2. Makes a "table reference" (TABLE_LIST) to parent the two tables.
  3. Assigns the join_using_fields/is_natural_join of the wrapper table
   using join_using_fields/natural_join of the rightmost table
  4. Sets join_using_fields to NULL for the right JOIN operand.
  5. Passes the parent table up to the same procedure on the upper 
   level.

 Step 1 overrides the the join_using_fields that are set for a nested 
 join wrapping table in step 4.
 Fixed by making a designated variable SELECT_LEX::prev_join_using to 
 pass the data from step 1 to step 4 without destroying the wrapping 
 table data.

 Problem 2:

 The optimizer checks for ambiguous columns while transforming 
 NATURAL JOIN/JOIN USING to JOIN ON. While doing that there was no
 distinction between columns that are used in the generated join
 condition (where ambiguity can be checked) and the other columns
 (where ambiguity can be checked only when resolving references
 coming from outside the JOIN construct itself).
 Fixed by allowing the non-USING columns to be present in multiple 
 copies in both sides of the join and moving the ambiguity check 
 to the place where unqualified references to the join columns are
 resolved (find_field_in_natural_join()).