You need to close the application first or you will get the .loc file included which may cause an issue. I suggest you highlight everything in the application folder then add it to a zip.
Also is there anything else going on? you may need to copy the license file I think its in Program Files\Common Files\ArchestraA\License
Are there any recipes/reports stored anywhere else?
It could be a bit more involved with driver installations that you will need for communnications etc