I've found that drag-and-drop flakes out (file doesn't show up in destination Explorer window, but attempt to re-drag gives a "do you want to overwrite?" message) if I click on the file *name* and drag it. However, it seems to work properly when I click on the file *icon*. I'm not sure what this signifies, and in any case it's a minor issue once you know the "click on the *icon*" trick.
This is on Win7(64)Enterprise, running BoxCryptor 1.5.405.138 Portable from a USB stick.