I can't answer the "why", but I had the same problem. I worked around it by 
putting the @Column annotation in the Primary Key class.


  | public class Foo {
  | 
  |   @Id
  |   public Long getFooId() {
  |   }
  | 
  |   @Id
  |   public Long getBarId() {
  |   }
  | 
  |   public static class FooPK {
  | 
  |     @Column(name="FOO_ID")
  |     public Long getFooId() {
  |     }
  |     @Column(name="BAR_ID")
  |     public Long getBarId() {
  |     }
  |   }
  | }
  | 

Seems to have given me the result I needed. But I'm not sure how this will 
affect future mappings, annotations, etc.

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