I just spent ages wondering why my latex document was not running bibtex when I compiled it.
It would be nice if some kind of error message came up saying that the reason there are unidentified references was because the project was set to not run bibtex. The check box for projects to run latex is easy to miss. I suppose this is along the lines of a general comment of it would be helpful to have more helpful error messages for relative novices such as my self. Otherwise it can be a bit of a mystery why latex isn't doing what you expect it to do.
Just a thought. Thanks very much for the excellent tool. My dissertation would not be what it is if it weren't for your work. Thanks.