My suspicions earlier were correct, the table body is an positional bounding box to resolve an IE7 bug. I'll be narrowing the fix to only effect IE7.
Otherwise we're between a rock and a hard place. That position:relative rule can't be removed- the only other workaround for the "positioned elem overflowing over background" bug in IE7 is using quirks mode which renders correctly. Redesigning the table headers to not use any positioning would effect several features (sort controls- and all their state and js, config panel launch button), require several days work and look significantly different than in other browsers.
As an alternative, because the tooltip js calculates its position relative to the browser window, its markup should be rendered outside a positioned container, even if the target of the tooltip is within that container. If this could be done the tooltip would not be clipped, and the markup efficiency of the tooltip could be increased.