If it helps to shed any light on it. If I don't fix that siteaccess's Home and then go repeat the same on another Home node, it gets a 3 instead of a 2 ie:
http://localhost/ez310/index.php/anothersite/Folder1
becomes: http://localhost/ez310/index.php/anothersite/3/Folder1
Talk about a jumbo sized order of the stupids with extra cream. It turns out that I'd used both RootNodeDepth and PathPrefix/PathPrefixExclude in my site.ini. This produces the above symptoms. Removing the PathPrefix/PathPrefixExclude pairing has fixed it.
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