My passenger side window (roadster) has been doing this for at least 2 years. It's still intermittent. Probably happens one out of five times but can be difficult to reproduce. Sometimes it clunks when it reaches the bottom of the track, sometimes it happens mid-way down and out of the corner of my eye I can see the window shudder, and sometimes it happens when I begin to roll the window up from a partially-lowered position (changing direction).

I hate random noises. Luckily it hasn't progressed very quickly.