We've received some direct support requests for this so I thought I would post a note here for all to see how to fix this problem. This information is also in the Important Skin Changes article.
The new colorbox version made changes to the CSS required to make it work. We took this opportunity to rearrange the colorbox CSS included in mojoPortal. The previous structure made upgrading colorbox more tedious. So, after upgrading you will need to replace your colorbox CSS references in the style.config file with one of the following:
<file cssvpath="/ClientScript/colorbox/colorbox-dark-1/colorbox.css" imagebasevpath="/ClientScript/colorbox/colorbox-dark-1/">none</file>
<file cssvpath="/ClientScript/colorbox/colorbox-dark-2/colorbox.css" imagebasevpath="/ClientScript/colorbox/colorbox-dark-2/">none</file>
<file cssvpath="/ClientScript/colorbox/colorbox-dark-3/colorbox.css" imagebasevpath="/ClientScript/colorbox/colorbox-dark-3/">none</file>
<file cssvpath="/ClientScript/colorbox/colorbox-light-1/colorbox.css" imagebasevpath="/ClientScript/colorbox/colorbox-light-1/">none</file>
<file cssvpath="/ClientScript/colorbox/colorbox-light-2/colorbox.css" imagebasevpath="/ClientScript/colorbox/colorbox-light-2/">none</file>
If you have any questions on this, please respond to this thread.