I got it working. It was a rookie error...when I restructured my character to have "Default" and "Seated" views I didn't realise it would lose all the rigging.
Now I've added back the rigging, it all works great!
Only problem is when he appears seated at his desk, it always appears in the same place, not necessarily where he's standing. That will be my next thing to fix.
Sounds like you are powering along. Personally I am a bit careful in putting too much in a single puppet. You can always have two puppets and hide one and reveal the other at transition points.
A problem that can occur is the mesh is worked out including hidden layers. So when the positions are too different, you can find body movements start looking “off”.
You can keep an eye on it by turning on the yellow mesh (an icon at bottom of scene and rig panels).
Just something to keep an eye on. Adding more alternatives in the one puppet can cause the old puppet to behave different.
Oh, structural changes triggering re rigging can mess up old recordings as well. So get the puppet right then don’t make big changes later. Create a copy of the puppet and modify that to be safe.
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I think making the Seated group independent is what keeps it from moving with the walk behavior. I did a quick example with the Walkbot puppet and this is what I got, using the rigging shown. I used left/right to start;/stop the walk behavior. When I used the immediately option, the sitting view also bounces when triggered.