If a PostgreSQL table has a composite primary key, Doctrine import ("generate-models-db") will only mark the first column of the composite key as primary. This is due to a bug in Doctrine_Import_Pgsql.
I have attached a short patch against the current 1.1 branch (revision 6580). The version 1.2 seems to have the same problem.
I have tested the patch with PostgreSQL 8.3.8.