It is not a permissions issue.
It is because any files viewed through a crypt remote are assumed to be encrypted (with the specified settings). Therefore any uncrypted files that try to be decrypted will just produce an error and not be visible. Definitely do not mix encrypted and uncrypted files or you will just have headaches.
It is not possible to show both crypted and uncrypted files in the same remote - you need two remotes. As Animosity says you could Union an uncrypted remote and a crypted remote to make it look combined (multiwrite-union will be available soon to make this more flexible).
But honestly - I think the simplest idea is to just keep them separare, and if you just want all your cloudfiles in "one place" you can just mount both remotes to a folder. They don't have to be mounted to drive-letters.
Is there a technical reason you need your files accessible in that spesific way - or is it more like a preference thing? If you tell me your motivation then maybe I can suggest other potential solutions to achieve the same goal.