Interesting. So I guess I don't have to worry about the submission i.e. the client would not face this issue.
This also points to the fact that it is a graphical error of some sort.
I'll keep trying to adjust the settings.
Thanks a lot for your help.
To answer your Q, I was taught by a fellow draughtsman to draft in this method of using layers on one dwg.
We simply play with viewports, and then freeze what we need/don't need.