Can you probe the 5MHz clock that you are providing and check if it is 5MHz as intended. Sinc ethe minimum interface frequency supported by FX2LP is 5MHz, we need to ensure it does not go below this value. Also, when you are using external clock, can you check the interface lines and understand what is happening across the interface?
Thanks Gayatri, I will be working on it tomorrow. I will contact cypress back if i don't remove this issue..