Suresh,
The MXI-3 extender is just a PCI-PCI bridge, so it should not affect any of the slots in your PXI-1000B chassis.
It would be good to try different MXI-3 boards, if you have more. Also you could try install other PXI boards (other than the PXI-6071E board) in slots 3 and 4.
If after doing this the board in slots 3 and 4 are still not being detected, there is a possiblity that the PXI-1000B chassis is damaged. In this case you will need to contact NI support (1-800-433-3488) to do further troubleshooting.
Claudia Lorente
Applications Engineer
National Instruments
http://www.ni.com