I experienced the same problem with SSIS and GnuPG for Windows (OpenSource PGP encryption tool), where the SSIS package would run locally but would not run when executed as a job by the SQL Server Agent. Two things solved my problem:

1. Because GnuPG for Windows stores encryption keys locally to the account that creates the keys, you need to login and create the GnuPG keys with the account that the SQL Server Agent will use when it executes the package.

2. In the SSIS “Execute Process Task”, I had to use a local path to the gpg.exe file vs. a UNC path.

Example, I used: "C:\Program Files\GNU\GnuPG\gpg.exe"

instead of...

"\\[server name]\C$\Program Files\GNU\GnuPG\gpg.exe”

Hope this helps!