It's random; it doesn't affect certain threads or certain forums. Sometimes it's a new subscription, and other times it happens when replying to a subscribed thread.
I have noticed that once a thread is loaded, the subscription option next to, "Get notified when others reply?" is sometimes "Immediate" instead of "Site Only (no email)". This is when the subscription gets set that way and I haven't noticed a pattern yet. I mean again, it sometimes happens to new subscriptions and it also sometimes happens when replying to existing subscriptions.
So the only real way to avoid the "Immediate" setting right now is by paying attention to what the setting is next to "Get notified when others reply?". For those of you who are not sure of where this is, it's always directly underneath the editor.