Which interface do you have? KEY or HEX series?
Can you clear the codes if you go to the specific module and clear it?
If you go to the about screen, is VCDS showing fully registered?
I thought the "Clear All DTCs" was available on the MicroCAN. It is not on a KEY interface. I need to check that for you in the office tomorrow.
Micro-CAN as well as KEY-series interface should have never supported the "Clear All" functionality, but I had gotten a similar report recently even though we never looked at it since the current version behaves as advertised.