Strange, I looked at the tests and all seems normal. I'm using the DB2Dialect and the annotations as above.
I ran the tests again with the same results. It works on 4.3.10.Final but I get the same primary key failure using 5.0.0.CR1, CR2 and CR3
I did some debugging and can see that sqlConstraintString() in the PrimaryKey class is called with DB2Dialect and when called for the "hibernate_sequences" table it has the column "sequence_name" defined as a primary key.
I ran the same test using SQL Server and the same SQL for the "hibernate_sequences" table is created, (with "sequence_name " a primary key), but that is accepted by SQL Server.

I will wait for the CR4 and then run a test again.