I have a many to may relationship CohortGroup and Employee. Any time I insert an Employee into the CohortGroup hibernate deletes the group from the resolution table and ins
As others have suggested, it's probably a problem with hashcode or equals.
hashcode
equals
Specifically: Hibernate proxies cause problems with instaceof which you are using in your equals method. That spells bad news.
instaceof
Check this out: http://community.jboss.org/wiki/ProxyVisitorPattern