About 5500 in 06? Looks about right IMO.
When you run 3DMark06, do you use the 'Analysis' or whatever it is to compare your results to similar systems?
Core 2 Duo e6600 @ 2.4GHz (stock)
Corsair ddr2-800 4-4-4-12 (stock)
X1900XTX 512mb (stock)
I get scores of ~ 6150 (1280 x 1024) - and that's apparently #3 out of 18 similar systems. So I don't quite see why yours are so bad?