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Allow me to make a Feature Request in the GitHub.

In admin, Store Settings, Layout tab, Layout Settings section, the setting "Display empty categories" should be "Yes" to show links to categories that might not have any enabled products.

While CubeCart can be made to work on Windows / IIS, it was never designed for this environment and is certainly not officially supported. You would be much better off switching hosting package / supplier so you use a Linux based system utilizing Apache Ian

If it works, don't fix it, right? Some general info you might find useful: Windows servers don't use .htaccess. Instead, all meta data regarding your site's behavior (including URL rewrites/redirects) are contained in web.config (as you've already noted.) The syntax is similar: a rule written for .htaccess can be used in web.config by just plugging in the values in the right spots, e.g. RewriteRule ^$ /index.php [L,R=301] equals <rule name="home"> <match url="^$" /> <conditions logicalGrouping="MatchAll" trackAllCaptures="false" /> <action type

CubeCart is not "very complex software" at all (try looking at Magento, OpenCart, Prestashop or most of the other packages) and is much simpler to use from an admin point of view than most. Is it missing a few things, yes of course but so does every single product out there but @Al Brookbanks does a fantastic job developing and maintaining this. There are many thousands of sites using it successfully including some with large large turnovers or taking hundreds of orders a day. The various problems you are having are likely down to how it was installed or upgraded and the hosting environment