I don't know about the problem you had with the top navigation, must have been some setting you changed in css.
I do understand the problem you are having about not seeing your changes, its because of the caching. I don't know why you deleted the log file as that won't do anything helpful. You can clear the server cache by touching your web.config (just download it then upload it that will recycle the app and clear the server cache), then clear the browser cache as well.
To make it easier, yesterday I updated the 188.8.131.52 release with some new config settings to make it easy to disable the cache while you are designing. If you downloaded the 184.108.40.206 release before yesterday afternoon, then you should download it again. You only need the new Web.config file and the /bin/mojoPortal.Web.dll. Replace both of those on your installation with the new version.
There are 2 new Web.config settings that can make it easier while you are designing your skin. By default the css is cached heavily both on the server and in the browser, and this is ideal most of the time. But when you are designing your skin this caching can be a hassle because you have to keep clearing the cache. Now these 2 Web.config settigns allow you to disable the cache while you are designing.
<add key="CacheCssOnServer" value="true" />
<add key="CacheCssInBrowser" value="true" />
Ideally you will set those back to true when you are finished designing your skin.
Hope it helps,