I have also faced this problem in my network and i found that there were some implementaion issues like,
1) If u r not using a dual band antenna, then there may be possibility that the 2 GSM (900 & 1800) may be facing in a different dxn or may installed in a diffrent cell.
2)And, there may be a swap.
FYI, we are using LAR=-80, LER=-95 & NBL=5.