A: 

Try Method 3 from this support article.

Change the SSIS Package ProtectionLevel property to EncryptSensitiveWithPassword. This setting uses a password for encryption. You can then modify the SQL Server Agent job step command line to include this password.

JP Alioto
Our packages all use EncryptAllWithPassword
Jon Erickson
+1  A: 

It turns out that the COM Interop assembly had issues running in 64bit (which the server was on) we switched it to 32bit and it ran fine.

Jon Erickson