Sounds like a bug…
Did you try with the latest version of InDesign CS6, v8.0.2 ?
I also believe this is a bug. I have experienced similar problems in exporting IDML files. If this appears to 8.0.2 please submit a bug against it.
I'll take a shot at updating to 8.0.2.
This may take some time since I'm not the admin for my machine.
I'll post an update as soon as I can.
Turns out I can't update it myself and the tech who can is out of the office this week.
For those who want to play along at home, tune in next week (Feb. 10) to see what happens.
Our tech updated InDesign to 8.0.2.
There is no change in the behavior.
I'll send a bug report to the folks at Adobe.
I have the same problem, did you get any answers?
I just ran into this problem, too. I noticed that only the items that were grouped on the master page PDFed even on pages where they'd been overridden and deleted. UNgrouping those items on the master page "fixed" the problem.
For the record, this even applies to masters based on masters. My A-Master has 2 grouped items. I based B- and C-masters on the main master, overrode, and deleted those grouped items. When PDFed, those grouped items show up on every single page created with the A-, B, and C-Masters.
This is definitely a bug, and a pretty darn annoying one. I often group things on masters when I know they will need to be overridden/deleted on some pages. This way, I can just override the group and I don't have to override them one at a time.
Ive had this problem a few times. Sometimes cutting and pasting the item back seemed to fix it. Other times, I just copied the document into a new document and it went away. Hope someone knows a real solution.
Yeah this is excruciating. One shape won't delete after overriding the master page items.., and in fact I can shift option select it and delete it.. but it just instantly regenerates before my eyes. 72 page catalog.. jeez.
I'll keep on the lookout for a solution. None of my items are "grouped" on the master page.
BTW.. This was happening with Adobe CC.. and is now continuing to happen in CC2014.
I upgraded to try to get away from the problem.
This problem is still there in Indesign 8.1. It's gone in Indesign CC 2015 (18.104.22.168)
I still regularly use CS6 (8.1) with many clients who refuse to upgrade to CC. I've not run into this problem in years. Are you sure you're all up to date?
I'm sure I am up to date, but the designer that created the file might not be.
But I'm the one that created a PDF from her file, and the problem is still there I'm afraid.