I think it is not related.

Of course, fossil should be using an ssh remote command execution within a non-interactive shell, a non-login shell. That should make the remote interpreter to avoid anything like the MOTD, or any welcome message the user could have set.

As fossil is not running ssh in such a way, welcome messages to the shell annoy. I could not find how to call ssh without parameters, without specifying any program to run. On the other hand, running "ssh REMOTE sh" (run the program sh) would make the shell non-login, so no displaying any welcome message. It could be used to overcome this login problem.

But the problem I seconded above was not related to any welcome message. Some repositories sync, some hang, between the very same computers.