I just set up a new bot and I'm having a very similar issue here too... rosterupdate seemed to work but it does not seem to have put people on notify; it does:
[BUDDY QUEUE] [BUDDY-ADD] Orgmember
[BUDDY] [LOG] Orgmember logged [off] <not on notify>
Logon notifies is set to enabled. If I manually do "!notify on name", it does seem to work and shows logon messages for that toon, but there must be an easier way. What am I missing here?