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Thanks for the support!
I'm still poking away at my tree structure. It's nice to have a static environment of 50,000 boxes, but a dynamic one is a whole different story. As expected, some slow downs occur when moving 5000 of the boxes around, however I haven't as yet optimised any of the "update" code (at the moment, I simply remove then reinsert each updated box from the root node). I could spit out some framerates, but they probably don't give much indication of what's under the hood considering I always try to get a high end computer. I suppose I should give out a little test app soon for other people to look at.