I've found a work around. This is not a pretty solution, but it works.
Essentially, the problem was that each banner was given an id, but these were the same id's in each instance of the banner - so the first top-banner was id="rp_post0", and the first sky-banner was also id="rp_post0".
To get around this, I made a copy of these four files:
rotating-posts.css
rotating-posts.js
rotating-posts.php
rp_admin.php
I renamed them and put them back in the SAME location:
rotating-sky.css
rotating-sky.js
rotating-sky.php
rsky_sky.php
Then, using BBedit I did a search and replace of every instance of 'rp_', 'posts', 'Posts', and 'POSTS' and replaced them with
'rsky_', 'sky', 'Sky', and 'SKY' (after checking the Case sensitive option in bbedit).
There are two other bits you need to rename:
function load_scripts()
function load_styles()
change to:
function load_scriptsSky()
function load_stylesSky()
I'm not really php literate, so I'm sure there's a better way of doing this, but I thought it might be worth posting until somebody posts a better solution.