I made the change to enable "continuous clock mode" according to http://www.cypress.com/knowledge-base-article/cx3-hardware-frequently-asked-questions-kba91295
However that does not fix the problem.
Additionally I need to call CyU3PMipicsiWakeup() to wake up MIPI-CSI2 RX block.
After this change, the code can go much further. I see SMState changing and got the first a few DMA callbacks.