In the document definition for hierarchical text structures you specify the record identifier in the Default value column. If a non-us-ascii character is included in that definition, Jitterbit 4.0 will write the UTF-8 encoded value instead of the Latin-1 encoded value as in 3.6. For backwards compatibility we need to convert it to the target encoding (which defaults to Latin-1).
The same problem applies for fixed width sources. And a correction: This applies to all fixed width text documents, not just hierarchical but does not apply to character delimited data.
This has been fixed in the 4.0.x branch (r52132) and will go into the 4.0.5.18 build of the server.