Currently, it is indeed not possible to use Boxcryptor behind a Zscaler proxy. Boxcryptor verifies the SSL certificate used to communicate with our servers at api.boxcryptor.com in order to prevent man-in-the-middle attacks.
Zscaler replaces our certificate to encrypt the data-in-transit with their own certificate so that their proxy can decrypt the traffic. This is actually a sort of man-in-the-middle attack which we protect our users from - and we have no plans to change that.
I'm not too familiar with Zscaler's configuration, but maybe you can exclude a domain from SSL inspection? If so, it should be enough to exclude api.boxcryptor.com.