In what ways do they behave differently?

Are the new objects being created in the exact same way? Position, rotation, distance between each other, are all the same?

Are you sure the objects are not being created inside of another object, block, etc?

Do the two physics objects share a constraint? If so, changing the angles or positions where they start could affect the constraint and affect how the objects react.

Is there any other code in your project that relates to the physics engine, such as affecting gravity?