Are you facing this issue for all the document. If yes, can you please send us one of your sample document for analysis. This will help us in isolating the actual root cause.
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I've just encountered this problem and resolved it thanks to Ohn's comment below. However I've narrowed it down further and discovered the only preference you need to trash is "InDesign Defaults", so:
~/Library/Preferences/Adobe InDesign/InDesign Defaults
Hopefully this helps minimise the amount of user defined preferences you lose.