Boxcryptor derives the total size and free space of the Boxcryptor disk from the hard disks where enabled locations are located. However, the reported free space can differ due to a feature in macOS called Purgeable Space:
When you check how much available disk space you have on your Mac, you’ll find that there’s a chunk of space that is not literally free, but is nevertheless available to applications. In macOS, it’s called “purgeable space”.
The purgeable space mostly consists of local snapshots of Time Machine, and also caches, sleep images, swap files and other temporary system files.
When an application requests more disk space than is currently free, the system automatically and instantly reclaims the corresponding amount from the purgeable space.
When retrieving the free space, Boxcryptor currently uses the raw information from the hard disk which does not know about purgeable space. I.e. while macOS considers the purgeable space as free space, Boxcryptor does not and considers it used space. We do plan to add support for purgeable space in the future.