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If you are able to set ID's native [Paper] to overprint something is seriously hosed and you should trash your prefs (see Replace Your Preferences). This is normally a problem with something at is set to overprint (usually in Illustrator) and then has the color changed, but ID has been able to detect this for native objects for as long as I can rememer and should be turning off overprint for white.
Thanks. I'll replace prefs and make an offering to the Adobe gods (maybe burn an old Quark manual?) in hopes it won't happen again.
Just to be clear: I didn't set paper to overprint. The attributes panel showed overprint but was greyed out so I couldn't uncheck it.
Still wondering if anyone else has had this occur.
As I said, it's not uncommon to see this in imported art, but it should not be happening with native objects to the best of my experience (I've tried on more than one occasion to make ID overprint [Paper] and a 0,0,0,0. swatch when trying to track down other user's reported problems, and never managed to do it). It's remotely possible that one of the effects might have an oversight that leaves the overprint on, but I've not seen it.
I just puzzled this out when the white letters on our new logo disappeared off the printer pdf.
Copied the logo to Illustrator, changed the overprint settings on the white and then pasted it back into InDesign and it was fine. Odd though, that I could not select just those white/paper letters and set them to 'not' overprint in InDesign.
You can trick it, select the problem white/paper element, that is set to overprint and change it to a different color, any color.
Set that new color to not overprint, then change it back to paper and it holds and will not overprint/dissappear any more. Faster than copying to Illustrator and back again.