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Both ZIP files you posted are version 2.5.3. If anyone else wants to look, the version number is defined near the top in common.py.
Whatever your problem is, it's not related to the plugins. The only thing I can think of that might cause this is if you're syncing your caliber configuration directory to Dropbox or SpiderOak or Copy or some similar service and something is going wrong with the sync process.
I recommend making a new thread in the calibre forum outlining what's happening and what we've tried here. More people watch the forum than watch this thread and someone else may be able to better help you sort out what's happening.
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