This is very odd, I can't think of anything obvious that would cause this.
One thing to check is that you are maintaining bi-directional
relationships correctly. If you change a ManyToOne ensure you also change
the OneToMany and vice versa.
There was a bug in the merging of new objects, which could potentially
cause an issue, perhaps like this, you may wish to try the latest 1.0.1
build.
If still now luck, please include the source for how you are changing and
merging the objects, and the class with the issue.