About a year ago, I started running into overprint problems with black in InDesign CC. It’s entirely possible that Adobe apps have always handled overprinting this way, but I swear that something changed with Adobe Creative Cloud.
By default, InDesign CC 2015 is set to display all blacks as rich blacks AND to overprint [Black] swatch at 100%. The Appearance of Black preference pane looks like this:
So let's say that we have a black rectangle layered over a 100% cyan rectangle. Onscreen preview looks like this, EVEN if you have Overprint Preview on:
Looks fine, right? Except overprint preview is completely lying to you. If you go to the Appearance of Black preference panel and change the output from rich black to "accurate" setting, you get this instead:
If you rendered a PDF of these boxes, the 100% black is going to overprint. That middle section will have both 100% black and 100% cyan.
Normally you control the overprinting of items with the attribute palette (Window > Output > Attributes), but with 100% black, the overprinting is controlled in the preferences palette. If you go back to the Appearance of Black panel and uncheck the preference at the bottom to overprint 100% black, it now looks like this:
Now, the black will knock out the cyan underneath it and the boxes will print as expected.
So what's going on? Basically, the rich black fools the overprint preview and 100% black is overprinted by default. Overprinting is happening and the preview doesn't show it.
I should clarify that only [black] is overprinted by default. Meaning that the default black, labeled [black] is overprinted. If you change the name of the swatch, even if it is still 100% black, it would no longer overprint.
You can change the preference for all new documents by opening the preferences with no documents open and changing the appearance of black settings. But note that the change won't apply to documents that were already created. If you open a file that you made a few months ago with the old setting, it's still going to be set to overprint black.
There are lots of ways to spot the problem. Overprint preview works if you have rich black turned off. The separations preview (Window > Output > Separations Preview) will also show you the problem. And you can take a close look at a press ready PDF.
Just be aware that this can become an issue if you are designing with black. It's easy to fix when you spot the problem. But you have to spot the problem first...