Using subkey instead of primary key

A client recently gave us a new public key to use.

When I try to encrypt a file from the command line in Windows with the new key, it states that it is using the subkey instead of the primary key, causing the client to be unable to decrypt the resulting file. This is causing a major issue in an automated process.

However, when I encrypt it by right-clicking on the file and using the context menu to encrypt, it works correctly and the client can decrypt it.

What can I do to ensure that the primary key gets used in the command line rather than the subkey?