Although not identical, this sounds similar to the triplication observable when using cygwin and boxcryptor 1.3.2 (mentioned in other post).
Now, unfortunately, the reaction to the post is not only similar, but identical, i.e. nothing. Obviously non paying customers cannot expect a fix (the other ones open a support ticket), but the least I would expect is an acknowledgement of the issue or statement of not supporting non standard or virtualized windows environments.
As a possible solution, try downgrading to 1.2. In my case the triplication is then gone and boxcryptor itself is faster. But afterwards I go so annoyed by another issue in combination with deletion of read only folders/files, which is according to the boxcryptor team an issue of windows. So I switched to encfs4win and there the issue did not occur so I think, the demonstrates where the issue actually was (I have not tested, but assume it is fixed in 1.3 release).
In summary I use now encfs4win an do have no problems, pc is based on win 7 32bit. For 64bit the dokan driver supposedly has some issues.
I may retry bc, but only after 1.4 is out and the issues are fixed.