Generate high speed data using GTX transceiver of Kintex-7 FPGA board
From the description of the working board (my emphasis):


  Reference clock for the serial transceivers of the carrier board is provided through the module's super clock  as well as a pair of SMA connectors for external pulse generators.


From the description of the non-working board:


  Reference clocks for serial transceivers are provided through 2 pairs
  of SMA connectors and external clock generator.


My reading of that is that you do not have a reference clock when using the SMA-FMC-LVDS board, and that's why nothing is working. You can add an oscillator on board (as you say) - it has to meet very tight jitter specifications if I remember right. Or you can inject (again a good low-jitter) clock onto the FMC connectors provided for that clock.