I guess there is some misunderstanding.
Due to the high-security standard of Boxcryptor, we only encrypt and decrypt files that are available locally - that means synced to your computer.
I assume C:\Users\NAME\Google Drive\Documents is your local sync folder.
By copying files into the Boxcryptor Drive (Z:\), you copy the files into the C:\Users\NAME\Google Drive\Documents but they get encrypted by Boxcryptor because you work within the virtual Boxcryptor drive (Z:\).
Because of that you "lose" 1Gb of storage.
The main issue is that Google Drive does not sync your files.
Please check your sync settings and enable syncing for these files and folders.
Best regards from Germany,