A score of 9600 is not a bad score to raise any system problem flags. Yes, it's lower than I've been seeing and can be affected by simple settings, background programs, and drivers especially since you bought it without an OS to install everything yourself.
3DMARK is NOT a system diag tool and has different versions. Try running other benchmarks like UT2K3 and try different video settings and drivers if high bench scores is your ultimate goal. Also watch the programs for anything taking resources. If real world apps and games are what you're concerned with, game on it and see if it's having any problems.