Try starting several instances in a batch file linking to different directories, e.g. using
start c:\programme\boxcryptor\boxcryptor.exe /multi /root <path to the directory 1> /mountpoint j: /label <label>
start c:\programme\boxcryptor\boxcryptor.exe /multi /root <path to the directory 2> /mountpoint j: /label <label>
Yours
A.