I think I had something similar to this a bit with my long termer back in 2004, and it wasn't the discs. It can be down to the suspension on that bike - have you been fiddling with the adjusters? Check all the adjusters are on standard and see if it still does it. Is it still on stock tyres? Are they in good nick?
I'm trying to remember when mine did it, but I think it was mostly when going quite hard, on track. It's a while back now though.
I'm not being as much help as I could be here, sorry. Will keep thinking.
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