This is one of the minor CSS problems that plagues me constantly. How do folks around Stack Overflow vertically align checkboxes
and
I usually leave a checkbox unlabeled and then make its "label" a separate element. It's a pain, but there's so much cross-browser difference between how checkboxes and their labels are displayed (as you've noticed) that this is the only way I can come close to controlling how everything looks.
I also end up doing this in winforms development, for the same reason. I think the fundamental problem with the checkbox control is that it is really two different controls: the box and the label. By using a checkbox, you're leaving it up to the implementers of the control to decide how those two elements are displayed next to each other (and they always get it wrong, where wrong = not what you want).
I really hope someone has a better answer to your question.