I've noticed a problem with tooltips in ui 1.9m1. When I hover over an item with a tooltip is displays correctly, but if I scroll down the page slightly and then hover over it again, the tip appears out of position. The further I scroll, the more tooltips are out of position from the element they are applied to.
It appears to be caused by a bug in jQuery 1.4.2 when setting an offset, which means that the jquery.ui.position plugin is affected and explains why tooltips are out of position. The bug has already been reported by someone else and I can confirm that the fix mentioned worked for myself: http://dev.jquery.com/ticket/6483
I can confirm that I was also having a *tonne* of trouble last night with both .tooltip() positioning and using .position() directly. I'm gonna look into implementing that change from the ticket and if it does indeed work, I'll submit a pull request.