When you upgrade, you should be taking the newly delivered web.config and re-merging your customizations into it (machine key, etc.), rather than keeping your existing web.config.
In 2.3.6.6, the following directive was added to web.config, and you're receiving this error because it's not in your web.config:
<add tagPrefix="portal" tagName="SkinList" src="~/Controls/SkinSetting.ascx"/>