I just noticed this and pointed it out to smichaud. It's possible it's not our bug at all, but rather Colloquy's or Apple's. I have a Minefield window open (displaying GMail), and a Colloquy window open in front of Minefield. Using two-finger trackpad scrolling in the Colloquy window, some of the scrolling appears to leak into the Minefield window. This is on OS X 10.5, smichaud is unable to reproduce, but he's on 10.4.
This is a bug in Colloquy; it leaks into *everything* that's behind it :P
Ah, I had no idea. Weird!