What is the interface between the FPGA and the FX3? Is it Slave FIFO? Backflow detected means that the DMA buffers in the FX3 are getting overflowed. This happens if the host is not requesting data as quickly as the buffers are getting filled. What is the host controller that you are using? Can you try with an Intel host controller. Also can you try with other UVC applications like e-CAM view.
It is better to create a tech support case for such debugging.