Before War Without End, Sinclair was the head of the rangers. The rangers were a large presence at the time and they should have gotten orders from him indirectly or at least talk about "Ranger One". But the only times people saw/heard about him is when he chose to contact them. Why is that?
Because he didn't want them to.
Sinclair is simply not in the habit of making a lot of public appearances. Even among his closest allies, as Ranger One he was notoriously cagey and kept to himself:
Marcus: Captain, if I were you, I'd quit while I was ahead. Back on Minbar, there was a saying among the other Rangers: "The only way to get a straight answer out of Ranger One was to look at every reply in a mirror while hanging upside down from the ceiling."
Whether it's because of his status as an agent of prophecy, something the Vorlons did or told him, or simply because of being an outsider among the Minbari, Sinclair just prefers to move in mysterious ways.
The series was called Babylon 5. The simple in-universe fact is Sinclair and the Rangers were not on Babylon 5. We shouldn't view his absence as anything but a narrative decision reflecting that fact. (Note Babylon 5 considers itself to be metafiction - an in-universe dramatization of "real" events in the Babylon 5 universe.)
Out universe the actor Michael O'Hare was having mental issues and we are lucky we got him back for War Without End.