What about third party plugins or utilities and other programs that run in the background? It sounds like you have a conflict someplace.
I used some startup scripts when this started to happen, but they are gone long time ago together with old Prefs, and crashes are not. No plugins. Background programs are usually TextExpander, BetterTouchTool and LogMeIn. I'll try to disable them though, thanks for a hint.
Also most of the time crashes happen when I start Indesign app itself, not when opening an indd file.
It seems with one of the latest updates to this date (08.05.2014) this issue has been fixed, although I haven't seen any note of something similar to this in Release Notes. My Indesign crashes no longer.
Also I stopped using LogMeIn recently, it's possible that this was the cause of the problem.