We are currently using Theme Builder 3.2.0, and Calendar 2.7.1.
In Internet Explorer 6, events that are not All-Day events are the same colour, even if they are on different calendars.
This is apparently caused by Builder, as the issue does not occur on communities which are not using the Builder theme.
The issue does not occur in other browsers, and unfortunately changing browsers is not an option.
Another interesting thing to note, is that if the builder-comments macro is on the page, adding a comment causes the page and calendar to refresh, and the event colours are displayed correctly.