In SOPC Builder version 7.2 , the system clock changes may not be saved to the SOPC Builder system file if the user clicks on other sections of the SOPC Builder GUI or outside of the SOPC Builder window before completely entering the new clock value. The GUI may display your clock changes, but it will not be saved to the .sopc file.
To comfirm if your new clock value was accepted, save and exit SOPC Builder after your clock changes. Re-open your SOPC Builder system to confirm the clock changes before doing more design work.
This has been fixed in version 8.0 and later.