How are you targeting the vertical alignment? Are you using priorities in the template or an end condition exception? I assume that you are setting your End Condition Properties to Target Type "Alignment XYZ" as shown below. Is this correct?
When you add points to your vertical alignment, are you simply using the command Geometry > Vertical Curve Set > Add PI? Then after you go back into Roadway Designer, none of the changes to the vertical are honored?
Is there any other relevant information that might help me to troubleshoot this issue?