Hi,
The uninstaller of version 2.0.401.166 had a problem in some cases which we have fixed. The weird part is that you have to update to the fixed version and then you can uninstall the application correctly. You can download version 2.0.401.172 here:
https://www.boxcryptor.com/download/Boxcryptor_Setup.msi
Sorry for the trouble,
Robert