I came across an interesting issue the other day with a Virtual Earth web part that we have developed. If you scrolled down the page and hovered over a pushpin, in IE the info window would be displayed higher than the pushpin, i.e. they weren't aligned properly.
I found the answer to my problem, the master page that the site was using did not have the following:
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
The missing doctype tag was putting IE in quirks mode and this caused the scroll behavior mentioned above. Heather Solomon has a discussion on Sharepoint master pages and the missing doctype. Unfortunately for us the master page couldn't easily be changed without making changes to a number of CSS classes.
I guess my point is that your sharepoint designer should know about this sort of stuff and design from the outset with the doctype tag.