Replaced the brake discs with official Brembo items on my SG9 2007 FSTi, because I thought the old ones were not flat - pedal judder. Super smooth for a bit, but then started pumping back through the pedal again.
Asked the garage to check: disc thickness variation 4-6 thou n/s and 3-4 thou o/s, but if I had to guess, it feels like judder on the off side and that side always has loads of brake dust on the wheel.
After they put it back on it was super smooth again!! But a few hours later, I tried braking from 70mph quite hard and it's back to juddering again.

Anyone experienced anything like this? Could it be a mounting problem? Just looking for ideas before going back to the garage in case it's a common Subaru thing.

I'd start by stripping and cleaning the brakes and checking for any sticking pistons. It sounds like you may have a piston sticking and heating up the disc

Jack it up and spin the wheels, if one is binding you will tell. Also is one wheel hotter than the rest after a drive? Might quickly diagnose which corner(s). Have to ask, is it like the ABS kicking in?

It's not like the ABS (which I used yesterday for the first time on a wet road after someone jumped the lights). It still brakes hard, but it's through the steering wheel as well as the pedal. Will check the heat thing carefully. Cheers.