Just a thought, are you changing down as you do this?, the rear will lock up quite easily due to the strong engine braking.
Nope I rarely do that. If I change down usually I don't use the brake until last few meter before stopping, because the engine braking is very strong on MT09.
That happens only when I need the brake - something happens and I need to use the front brake in a sharpish way.
Update today I was overtaking few cars with 70ish or more and I was in the opposite lane while doing that. The lane was straight and free more then 500-600 meters ahead. A car has popped up from a driveway in front of me in the lane. Luckily there was enough distance. The front brake was pulsing hard at the lever when braking from speed and the whole front was jumping like going through speed bumps.
Any ideas?
I had what i used to describe as a pulsing/juddering sensation on my bike for months which i couldn't figure out which was doing my head in, and the only thing i had left to try was changing the braided brake lines that were on the bike and they turned out to be the culprit.
The previous owner never really looked after the bike and they were either most likely damaged or possibly just faulty, but once changed to a new set everything was sorted.
Before that i'd more or less replaced the whole front end of the bike spending a lot of time and money in the process, ie: head bearings, pads, discs, forks, but because they were aftermarket brake lines, and braided, i just never thought they would've been the solution.
Dunno what lines you have on your bike, but i'd imagine there's an even higher chance of this possibility if they're not braided.
I'm not saying this is your problem, but it's certainly an option to consider and not rule out as i did.