If Notes embeds a Sametime client connected to Sametime in Connections Cloud, there are limitations on showing presence in Notes Apps.
The reason is that Notes Distinguished Names ( CN=User Name/OU=Org/O=Company) are stored in Notes Forms (example: From field in Inbox Message) but cannot be found to pick up presence by the Sametime Server.
An option today is to modify the inbox columns and forms to use Name([CN];From) instead of "From" to only search for the common name instead of the DN.
It would be much easier to just have an option in the embedded Sametime to check a name format and replace the search string just with the common name.
A single checkbox would remove the need of changing the design in multiple places.