I just looked into this on my machine. We had updated to a newer version of Nivo and it looks like things changed a little. Before we could change a nivo theme just by changing the css file but now it seems a little different because they use different css selectors in the themes. For example the light theme has selectors like this:
but since the class them-light is not in the markup that selector won't work.
One way to fix it in the current release is to go to the settings for the gallery and under Miscellaneous put theme-light for the custom css class and now that selector will work and the style will be applied.
However I think for the new release of mojoPortal I can fix it by removing those theme specific selectors so that all the themes use the same standard selectors and just changing the css file will change the theme. Maybe I did that with the older version of Nivo and forgot to do it again when we upgraded to the newer one.
A new release is coming soon so this will be fixed soon.