When viewing an Inventor file in thin client, you only see the master design representation.
When you publish a dwf from Inventor you get to chose the representation:

The jobprocessor always takes the master design view representation.
Unfortunatly, when you add some colours a new default design rep is created but not included in the .dwf created by de jobprocessor.
How I want it to display:

How it is displayed in thin client:
