If your CPU has a FSB of 1066 then in the BIOS it's best to leave Auto settings, and first populate the 4GB stick in the DIMM slot closet to the CPU (DDR3_1).
If you have a 2 different sticks of RAM then sure that can pose a problem, both sticks should be the same Frequency, CAS Timings, Capacity (GB), and Voltage. Try one (1) stick at a time.