OK, I'm running WPMU 2.8.6.
When users auto-register to a sub domain blog, they receive the activation email but never the second Welcome User Email. However, a user receives both emails if registering on a top level domain or if a moderator creates their account.
I've tried deactivating all plugins, to see if one is interfering, but this doesn't help. Any ideas or places to start looking - hunting back through previous support emails, this particular feature seems to have regularly broken in previous releases of WPMU.
I can't yet upgrade to 2.9.2 as I'm running this on a critical client website up until the end of May.