I find this scenario rather irritating: I get to orbit, I may or may not do some manual maneuvers to rendezvous with something, and then I decouple the final launcher stage... and suddenly I'm hearing "click-click-click-click-click-..." as MechJeb triggers a series of stages in order to get to one that has engines activated. I don't want those engines active yet because I may be about to perform a docking or something else and I don't want to accidentally throttle them up by hitting the wrong key. And I certainly don't want it decoupling anything! (Fortunately the engines come before the decouplers in this rocket.) But my only option to prevent this from happening is to disable auto-staging and then re-enable it for the next launch, which I generally forget to do because I'm used to MechJeb 1.9.8 where it wasn't a problem.

In my opinion, if auto-staging is to be a global setting, it shouldn't occur unless running an autopilot function which uses the main throttle. Alternatively, if people want it to happen while flying manually, then it should not be a global setting - instead we should be able to independently toggle it for each autopilot module, with a separate setting under thrust control for auto-staging during manual flight.

Seconding this, I've had a couple of my ships decouple themselves to pieces in orbit because of this issue.

Same here, I find myself having to set up reminders so this doesn't happen.

Can confirm this as well. Fortunately it hasn't cost me any missions, but it can be startling.

Auto-staging is intentionally a global setting, but we are still lacking the interface to let you set it to be active always/during autopilot functions/during ascent/never. We'll get this in sometime soon.

So, it will be a "global" setting that lets you select which cases it's active in, rather than independent settings for each of the cases in which it can be active? I don't see the difference, really, and making it one global setting with lots of options sounds like it could be more confusing and less flexible. If there was one window showing all auto-staging options, what I would do is put one checkbox for each module or mode:

Auto-stage during:
* Ascent Autopilot
* Maneuver Execution
* Landing Autopilot
* Manual Flight
Delays: [ 0.5] pre, [ 1.0] post

etc. Then each autopilot module that currently displays an auto-staging checkbox would simply display the one that applies to that module, keeping things clean and simple. But I'll wait and see what you do with it.

think this got done a long, long time ago.