Smiler... you hit the nail on the head... the bit of scrap I was using wasn't MDF but some 19mm ply offcut left over from when i made my workbench. And it had warped over the last 6mo stored on end in the garage. Not much, maybe 1.5mm curve over a 500mm length but enough.

Anyway, I took the plunge and drilled the actual table and fitted it. Works a treat, so all tightened up and runs smooth, although these linear bearings aren't as silent as I'd imagined they'd be. The table runs parallel to 0.1mm and horizontal to 0.05mm over its run, and deflects 0.15mm with 4.5kg load in the centre so I think that's pretty good.

I don't like MDF tho, drop a bit and it bruises so easily, look it it wrong and it flakes. I definitely will make machine #2 with ally or steel...

Right I'm going back to the garage to start on figuring out how the leadscrew is going to be mounted. I have an idea on that, but that's going in another thread.