Cause of issue: ECC only sends delta changes. CRM deletes all classes and reload whatever that are sent by ECC. So, this resulted in only partial data in the system. Initial creation of the material also did not bring through the classes until a change is made.
Solution: We create a new program and assigned to event 00004002 in table TBE31 in ECC. This program basically always pass all the classes for the material to CRM.