I made a conscious choice to use this list method, so that it would be more SEO friendly, as search engines usually aren't to bright regarding URLs that have been generated by javascript.
To correct the category ordering issue, it would be good to find all
instances in the PHP code. Any variables that are being created (the first item in the parentheses), prefix with list_
Then, go through the TPL file, find any variables in that files, prefix each one with list_ (after the $ symbol, if it exists).
That should likely take care of the issue for you.
Simple updates to this project will remain free, I do intend a Pro version as a commercial release
