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Seems to be a bug, same problem here: Re: Forced line breaks on variables don't turn to spaces
But it seems to be fixed, for I don't see this issue in InDesign 2017.01 / Build 184.108.40.206
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Did you try updating InDesign to 2017.01 / Build 220.127.116.11? Are you still facing this issue?
No, I have not updated. The lack of contrast in the new UI color schemes is headache producing, so I had to go back to the older version. I have used paragraph indents to force the line flows the way I need them so I can remove the forced line breaks. That appears to have worked for now.
If you have fixed this issue in the newer versions, then I hope at some point you put the UI back to usable color contrasts. I may be stuck with 17.0 for a good long while else. I live in InDesign, so usability of the interface is far more important to me than bug fixes that may affect a small portion of my work flow.
Yes that is a bug within InDesign...(Running headers are designed in a way, to convert all line breaks to a single line.. but the issue you pointed out is certainly a bug)
I was able to reproduce it with CC 2017 though.
I would like to add that although the UI may not be very pleasing to you (but we are improvising on it in the upcoming release), each release comes with its own new set of features. I hope you give it another try:)
Like someone correctly posted above, please use the workaround at Re: Forced line breaks on variables don't turn to spaces for the time being.
InDesign Engineering Team