In hibernate 4.3 org.hibernate.annotations.ForeignKey declared deprecated in favor of JPA 2.1 javax.persistence.ForeignKey.
But JPA annotations ignored sometimes:

for annotation:
@JoinTable(name = "SPL", //
joinColumns = @JoinColumn(name = "SPL_POJO_ID", foreignKey = @javax.persistence.ForeignKey(name = "SPL_FK_POJO")), //
inverseJoinColumns = @JoinColumn(name = "SPL_SUB_POJO_ID", foreignKey = @ForeignKey(name = "SPL_FK_SUB_POJO"))

following schema is generated:
alter table SPL
add constraint FK_5nufiopmkmxpku6ash397jpwe
foreign key (SPL_SUB_POJO_ID)
references SUB_POJO;
alter table SPL
add constraint FK_23dp68pb6mw3oynxgs5lfdutf
foreign key (SPL_POJO_ID)
references POJO;

schema generation works as expected:
alter table SPL
add constraint SPL_FK_SUB_POJO
foreign key (SPL_SUB_POJO_ID)
references SUB_POJO;
alter table SPL
add constraint SPL_FK_POJO
foreign key (SPL_POJO_ID)
references POJO;

with old annotation:
@org.hibernate.annotations.ForeignKey(name = "SPL_FK_POJO", inverseName = "SPL_FK_SUB_POJO")

example project attached