On your production site you really don't want to be having all those css files loaded separately that is not good for your Yslow/Page speed score because each one is another http request needed to load the page and that slows down the page.
You should let mojoPortal combine and minify the css and you should enable caching by keeping these settings:
<add key="CombineCSS" value="true"/>
<add key="MinifyCSS" value="true"/>
<add key="CacheCssOnServer" value="true"/>
<add key="CacheCssInBrowser" value="true"/>
That said, it should resolve the urls correctly when you load them separately, else I would consider it a bug. What version of mojoPortal are you running? You can find the version under Administration > System Information
Hope that helps,