Following sequence:
1. on iOS: Take e.g. a pdf file or any other file type e.g. in mail app and send it to Boxcryptor via extension.
2. Authenticate to BC and choose a folder in Dropbox.
3. Upload the file as "encrypted" to the selected folder. File name encryption in the BC-settings is enabled.
4. The file appears normally in the folder on the iOS app an can be opened, deleted etc. and DB syncs it with your desktop.
5. Open the Dropbox client on Mac and go to that folder.
6. The uploaded file is not visible there.
7. If you go directly into the Dropbox folder (without BC) then you can see there the file with the encrypted file name, but it has a white icon (usually it has a black icon).(Seems to me that the filename encryption on iOS works differently compared to OS X?)
If you do the same sequence and disable filename encryption on iOS, everything is fine. Also the sync from OS X to iOS works fine with encrypted filenames enabled on the OS X client.
My Setup:
iPhone 6 w/ iOS 8.3, BC client 2.4.407 (575)
Yosemite 10.10.3 with BC client 2.1.435 (654), DB client 3.4.3