The answer is: "It's a feature not a bug". Windows can handle filenames with up to 32.767 characters and so does BoxCryptor. However, many other programs do only support filenames up to 260 characters - even many Microsoft programs like Windows Explorer and also Dropbox.
It is not possible to avoid this behavior at the moment, but we're thinking of adding an option to only allow up to 260 characters.
PS: You do not have to boot Linux to handle those files. There are other file managers for Windows which can handle those long filename lengths, e.g. xplorer² (http://zabkat.com)