Hi Aussie mate,
I think I may have a sense of what's happening, although I'm having trouble duplicating it.
Sean's xml is for a single command and not a group. Commands can't "float" -- they must be put in a group, whether you create one first and then paste in the command or whether it gets pasted into an existing group.
You can't paste a command into "empty space".
By using the ctrl-v method, you're guaranteeing that the command is being pasted into an existing group because something must be selected. With right-click, it's possible to paste in empty space depending on how big your command tree window is.
I *think* that in this scenario, you will only see the paste option rather than the full command context menu that you would see if pasting properly into a group. So that might serve as a cue of what's happening. But if ctrl-v is working reliably for you, then perhaps that's the way to go.