This is a known issue with the Video Timing Controller Software Driver v3.00.a in ISE 14.3 and Vivado 2012.3.
It is due to a missing function call in the metadata for the driver to handle multiple instances.
This causes the driver to default to a single instance.
This driver fix is included in ISE 14.4 and Vivado 2012.4 Design Suites.
To obtain the fixed version of the Video Timing Controller v3.00.a software driver, click on the ZIP file below to download the "ar52666_video_timing_controller_sw_v3_00_a_14_x_2012-10-30.zip" file.
For information on how to use the driver with the Xilinx SDK, see (Xilinx Answer 32309).
For a detailed list of LogiCORE IP Video Timing Controller Release Notes and Known Issues, see (Xilinx Answer 32754).