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reset your preferences -
adobe media encoder: https://forums.adobe.com/thread/1713540
after effects: http://helpx.adobe.com/after-effects/using/preferences.html
muse (mac): https://forums.adobe.com/thread/1246022?tstart=0
If the prefs reset doesn't solve the problem, please post the ENTIRE InDesign crash report on Pastebin.com and put a link to it here.
You also need to run the updates for all the programs in the suite...