I've had an intermittent problem since upgrading to v.2.0.417.367, and only since upgrading.
I have filename encryption enabled. I'll edit a .pdf file in the Boxcryptor drive and save it. Then I go to another directory in the Boxcryptor drive and then go back to the folder where I edited the .pdf. And that .pdf will be missing, but there will be a file with a scrambled name (the Chinese characters one would see when viewing the folders outside of the Boxcryptor drive) and no file extension. If I give it a .pdf extension and open it, I see it's the original file and can rename it to its original name. No changes are occurring outside of Boxcryptor's drive.
This is happening within a SugarSync (v.18.104.22.168340.20140226) folder within the Boxcryptor drive, btw. And I'm on Windows 8.1 x64.