I am using a FMC Samtec_ASP-134486-01 connector for GPIO connections.
While importing the netlist all the other components are connected to correct nets but the FMC connector remains unconnected to any net.
There is no connection to FMC.
Creating and importing netlists has been deprecated for4 or more years now. The recommended method now is Schematic Editor / Tools / Update PCB from Schematic [F8].
Also:
V6.0.9 is getting a bit old, and several bugs have been fixed (I believe V6.0.9 has a nasty one with net labels in buses). The current is V6.0.11. The 3rd number increments are for bug fixes and updating is always recommended.