The alignment of the name in the top pane shifts when going from bold to normal, which you'd expect, but as the thread gets deeper the shift changes from (looks like) centred to moving the 'name' text over to the right by an increasing amount. I first noticed it on the Usenapp announce thread in UCSM, about 10 deep. With two messages at the same (10+) level, marking one read makes it visually a whole level deeper than the other due to the shift - see pic, both my messages at the bottom there are actually the same level.
Anchor the first character would probably be the best looking solution.
(neat image attach btw!)