Yes, I use my own stylesheet without problems, but with 'modern' themes don't serve modify startup.html because they use their own classes (see the file themes.props)
What I do is to import my styles in their stylesheet.
For Example, for theme Clifton, I change the file 'C:\AwareIM\Tomcat\webapps\AwareIM\aware_ext\resources\css\clifton-all.css' adding at the end
@import "mycustomstylesheet.css";
For themes w8 had to change the file azurra-all.css
