A BoxCryptor folder appears to be recognized by the BoxCryptor application by the existance of the default configuration file (.encfs6.xml) in that folder. If you create a BC folder and then choose to locate (and possibly rename) the configuration file in another folder, the BC application, when run on another computer, will not find this folder.
This is a issues that needs to be corrected in this application if we (the users) are to be able to re-locate the configuraiton files - something that I think is wise from a security perspective.
I ran into this when...
I created a BC folder on SkyDrive on my home computer and subsequently re-located the configuraiton file to a local folder on that computer (I just don't think it's wise to leave un-encrypted encrypt/decrypt configuration files in the very folder that you are encrypting). Anyway, that worked fine on my home computer. However, when I went to setup this folder on my work computer, the BC application could not find my BC folder on SkyDrive or, if I used a Custom to select the folder directly, the BC application did not recognize the folder as being a BC folder.
Workaround: Temporarily put the expected configuration file (.encfs6.xml) in the BC folder so that the BC application will recognize it and allow me to define and mount a drive to that folder and then redirect that drive instance to thereafter look for the configuraiton file in a specified local folder on that computer. Finally, remove the default configuraiton file from the BC folder.