Same problem with hibernate version 4.2.8.FINAL.
My case is similar:

@Entity
@Table(name="LETTERS_OF_GUARANTEE")
public class LetterOfGuarantee extends EntityBase {
    @ManyToOne(optional = false)
    @JoinColumn(name="CUSTOMER_ID")
    private Customer customer;
    ...
    ...
    @CollectionTable(name="LETTERS_OF_GUARANTEE_AMDC")
    @ElementCollection(fetch=FetchType.EAGER)
    @Column(name="AIRPORT_ID")
    private Set<Airport> amdcAirports;
    ...
    ...

After ddl, the following primary key is created as expected:
PRIMARY KEY ("LETTER_OF_GUARANTEE_ID", "AMDC_AIRPORTS_ID")

Also, another unique index is created (which is not expected because this does not allow records with the same AMDC_AIRPORTS_ID across the table. Not only for the same master table ID):

CREATE UNIQUE INDEX "UK_NDKRX9Y79EWUPQCCJV522DNQW" ON "LETTERS_OF_GUARANTEE_AMDC"
(
"AMDC_AIRPORTS_ID"
)