I'm not sure whether a few problems we have are somehow related to this one, but BC or more likely? CBFS seem to cause at least some problems when both temporary files and BC's filename encryption are involved :
Windows XP and Windows 7
BoxCryptor 1.5 Unlimited
When files are rsync'd to BC's volume ( Z: ) and filename encryption is turned on, there are many "permission denied" error messages generated by rsync. These errors have to do with temporary files starting with a '.' (dot). In addition, we also get "No such file or directory" like error messages.
Software tools often store temporary files in source or destination directories, in this case BC's destination directory. When we tell rsync to use another location as a temporary directory, i.e. not part of BC's volume ( Z: ), filename encryption still turned on, most errors are gone, only a few error messages are left.
We disabled filename encryption already for quite some time, use a non-default temporary directory (not part of Z:), and haven't seen any error messages yet.
Well, we probably should have researched this problem a bit more detailed, haven't found the time yet, but maybe these observations are already of some use ?