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1b1ed1a
(Get the code!)
@JP, OK, so definitely the RTree.
I've rewritten that routine a bit to always (well, except in the cases of UR_DELETED and UR_NEW) do both a remove and an add, and removed the medium-big hammer (UpdateAllItems()) at the end.
Seems to work for me, but then the last one did too, so if you could test it a bit that would be great.