When building the IssueTrackingLite sample, setting the CSS file on the root node will produce a bunch of "Could not resolve 'master-color'..." warnings.
The only way to avoid that is to set the CSS and assign the 'theme' style class to the root AP right at the beginning. This is what is done in the Tutorial, I think, but is totally unnatural if you build the sample to give a demo of the tool for instance -- you typically set the CSS at the end.