The path to encryptionKeyFile option has to be a full/absolute path when using --fork option where as other options will resolve the relative paths when using the --fork option.
See attached logs
This is similar same issue but different parameter fixed in
https://jira.mongodb.org/browse/SERVER-8524
"it's because --fork changes the CWD. We are doing something special in the code to convert the relative paths for dbpath and logpath into absolute paths. We will have to do something similar for the SSL paths"