I am posting this thread on behalf of a friend although I did suffer from a similar problem myself.
After approx 4500 miles my GSX-R 600 K5 started to suffer from front end judder under braking (beit heavy or moderate braking) speed was irrelevant as it happened at high speed and moderate speed. You could feel it through the handlebars and through the brake lever. I never got to the bottom of what the cause was (although I did report it to my dealer) as I decided to upgrade to a 750 K7.
Unfortunately a friend of mine with a GSXR 750 K5 has also now got the same problem.
We have checked the discs for warping (using a DTI and not just visual), wheel bearings and have changed the front pads but with no improvement. In fact it appears to be getting slowly worse.
I have researched forums on the net and have found reports of front suspension issues with the K5's.
An email has been sent to Suzuki and we are waiting for a reply. In the meantime can anybody throw any light on this issue.