Double-check the PDF - it may not have those boxes defined. Quark is very naughty about that.
It's a beautiful thing that INDD can place and handle PDFs. But I must say, it really seems like it is being abused these days.
For those who have worked in prepress long enough, remember what used to happen with nested EPS files?
I know PDF is "different", but the integrity of the process begins to deteriorate working this way.
the PDF is fine, I created it and it works in CS3
I think he means that you're prisoner to whoever created the pdf. Did they embed fonts, did they use the correct color usage for your job, are the images hi resolution, etc.