Lijo,
Adding to what Fred said, have you measured what the cable loss is? Usually we see 1-2dB loss in the cable itself from the SMA to the spectrum analyzer. Also, if the SMA connector is not part of the board and soldered ON, how the SMA connector is soldered too becomes critical. i.e. the ground of the SMA connector should be soldered close to the RF path ground, this ensures shortest return paths and keeps the impedance unchanged.
You can friend Fred or me and then send us your reference design privately. Sometimes poor layout too can reduce the performance of the board.
