In general, (XML) Schemas have a so-called Namespace URI which also affects the Components based on the Schema.
In Tridion, this Namespace URI is a property of a Schema. You cannot edit it directly, but it is obtained from the XSD. The default Namespace URI for newly created Schemas is a UUID (to ensure it is distinct from any other Schema).
The reason for this introduction: if you port a Schema between environments, its Namespace URI does not change. This is fortunately so, because changing the Namespace URI of a Schema on which Components are based has potentially huge impact; it effectively invalidates all existing Components based on the Schema.
I guess you are first manually creating the new Schema in both environments (effectively resulting in Schemas with different Namespace URIs) and later porting the Schema changes, resulting in the Namespace URI getting in sync between the environments (but a one time change on the target env.) ?