1. To color the progression text, you need to change the css - look under Customizing the script under Progression box, I've tried to break down what each css selector controls. I looked at your page and the ".dim { opacity: 1; filter: alpha(opacity=100); }" needs to be between the <style></style> tags in order to work.
   
   Another problem might be that the tooltip css is missing. Add this to your custom css (Control Panel > Custom HTML & Script > Custom CSS > CSS Additions to Standard)
   

   .tooltip, .preview, .screenshot { cursor:pointer; }
   #tooltip, #tooltip2, #preview, #screenshot { color:#dddddd; background:#222222; border: 1px solid #333333; padding:5px; display:none; opacity: 0.9; filter: alpha(opacity=90); text-align:left; border-radius: 1em; -moz-border-radius: 1em; -webkit-border-radius: 1em; }

2. When you first upload a file into the file manager it gets saved to the site, but the browser itself doesn't know it needs to look for a new file (the file is cached). So you need to reload the page, maybe twice, while holding down the shift key and clicking on the browser reload button - this tells the browser to refresh its cache. If that doesn't work, then click on the file in the file manager so it opens in a new tab, then reload it directly from there... if you still aren't seeing the updates, then re-upload the file.
3. This might also be an issue with the tooltip coloring. Try it and tell me if you are still having problems.

<script src="http://www.axiomfiles.com/Files/258012/tooltip.js" type="text/javascript"></script>