Jot server is a small server app on its own and has nothing to do with the UNA system. Therefore Messenger Module is running independently from the whole UNA framework. If you have problems with connection of your jot server you either check your ssl certificates if they are valid or the communication port on which your jot server is listening to (commonly 5000). Those are the main issues people have to deal with when having problems with jot server setup.
Edit: If you cannot solve it on your own, I know from my own experience, that Alexey, who is the Master of Messenger mod of the UNA team ☺, is always very supportive when somebody is having problems with the setup.