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that's an old bug, that perhaps was never fixed. Or it wasn't fixed before InDesign CC v9 ? I'm not sure…
What is the exact InDesign and OS version you can see this behavior?
Best is to leave the hands off the keyboard and the mouse, if you run an export to PDF script.
In my old tests even one single click with the mouse forced the bug.
See also this old discussion here:
Thank you Uwe
My OS is win 7.
my inDesign vision is CS6 and CC2014.
That's really bad…
Do you have a chance to test with InDesign CC v9.3.0 and InDesign CC 2015.3 ?
Back then I couldn't force the bug with CC v9.0. But I am on Mac OSX and that bug could well be sitting there waiting all the years to hit with all the Windows versions of InDesign since CS4. (Sigh.)
So far what I have is CC 2014.