Based on what I have seen, the core reason for this behavior deals with the theme being used on the site. The best way to test is to switch themes temporarily and see if this solves the problem. Now, changes are that if this is related to the theme, you need to check to see if they do things to enable PNG support in IE6. If so, then that is the cause. You need to then edit your theme to disable the functionality that allows IE6 to support PNG files.
You could probably find more detail on the Google Maps Groups/Forums.