I am using v7 and if you make changes you have to save the c2d file. I have not used the save gcode yet so not sure what they are saving and where. Part of the v7 is if you make changes in the design and quit the CC application you should get prompted to save the file. If you make changes and leave the application open and then go to CM that might be what is going on with not saving your changes.
Try saving the c2d file before going to cm to see if that fixes your problem. If it does not report it to support and the thread on v7.