I've seen lots of stuff on here about "oh your discs must be warped" but thought I'd be optimistic and see if it could be something else.
I took the pads and discs off (well one disc - the other was wedged on too tight and I didn't want to damage it getting it off as not replaced it). I exercised the pistons a bit to make sure they weren't seized. Used brake cleaner on the pistons, calipers, pad plates etc to get rid of any build-up of brake dust. Checked the discs which seemed to spin straight and didn't seem warped. With the one I got off I cleaned the hub behind it to make sure it was sitting on there correctly. Oh and I left the anti-squeel shims off when I reassembled them. The EBC pad instructions say not to include them. I think I read the instructions after putting them on the first time.
Anyway after just checking, cleaning etc the brakes are now fine. No judder.