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I think I'm having similar issues. I'm trying to tweak some perspectives. I've ordered my contexts in the sidebar in a specific way to prioritize the way items sort.

First, I have a main context of Home with various sub-contexts. Next I have a sub-context of Computer with various sub-contexts. Then assorted other contexts.

Sidebar:
Home (main)
Home Office
Home Kitchen
Home Bathroom
Home Garden

Computer (main)
Computer iTunes
Computer OmniFocus

If I set:
Context: Remaining
Grouping: Ungrouped
Sorting: Context
Available/Any/Any

I get:
Computer (main)
Computer OmniFocus
Computer iTunes
Home (main)
Home Bathroom
Home Garden
Home Kitchen
Home Office
...other random contexts

If I just change the ungrouped to group by Context, the order of the contexts is:
Home (main)
Home Office
Computer (main)
Computer iTunes
Computer OmniFocus
...other random contexts
Home Kitchen
Home Bathroom
Home Garden

So with the second scenario, the Home sub-contexts are in the right order, and Home is properly above Computer, but I can't figure out why the other random contexts are in the middle there and why the Home Contexts are split up. I thought it might have to do with which contexts have active actions and which don't, but that doesn't appear to be it either.

The ungrouped one has me completely baffled.

Is expecting them to show up in the sidebar order incorrect in either or both of these instances?