You can have a similar malfunction, as I found out the hard way, if you adjust the pushrod to eliminate too much of the freeplay, you can accidentally adjust it to the point that the master piston is being pushed just past the bleed hole. The rear brake will still seem to work properly... braking and releasing as expected. But as the fluid heats up a bit, the brake will get applied increasingly until it locks up. Then the only way to release it is to shorten the pushrod back to normal.
As a side note, there is no rebuild kit for the rear master on your bike, and there is little to no availability for good used ones anymore. Every one I tried 10 years ago was pitted. But luckily, you can modify a Ninja 250 rear master to work without too much trouble. You will have to fabricate some spacers and modify the pushrod, but it works great... like new.
