Hi and thanks Bob for the link but I'd already seen that.
As per the last comment in the thread from 2013...
I still can’t get the extra boxes to disappear when I PDF my indesign file to upload. My Simulate overprint box won’t even light up to check and try.
Is this a new problem with CS6?
It's probably a limitation of the printer that they can't simulate overprinting. It's not something InDesign can do anything about.
You'll have to NOT use spot colors with transparency, in that case.
have you tried changing your PDF compatibility? i remember to solve similar problems by using 1.5, but try others too.