Slick-C profiling captures the time spent in the Slick-C interpreter. Most of the work is done there, so it is helpful for finding bottlenecks, but there is work, like color coding, drawing, and other bookkeeping that Slick-C has no part in.
I think I may have stumbled onto the problem that you were seeing though in the course of solving another problem. There will be a fix in RC3 that could help.