I use BC on two MacBooks and sync via Skydrive/OneDrive. After a few weeks started getting file conflict errors - I found that one of the Macs' BC had switched on filename encryption! I then switched off, deleted the files and restarted sync.
I just restarted BC on the second Macbook and the same thing. FileEncryption got turned on in the background again.
Can you please stop changing preference settings to back to defaults when BC gets restarted? I make changes to the preferences as they are my preference. Preference changes at the moment (version 2.0411) are not persistant and revert back!