I recently got my Power FC installed in my R33 GTST. I had the same problem to start with but the light stayed on all the time not flashing. This was because my boost control warning sensor was turned on when i didn't had the boost controller kit.
when i was on the high rpm like 6000, the engine check light started flashing as the knock reading was like 89-97. So i had to take my car for dyno tuning again. If you are getting the high knock reading, Check your map on the power fc and locate the point on the 20*20 cells when the light flashes. You have to reduce few degrees on the timing from that cell and the neighboring cells as well.
I am still getting same problem but its not due to knocking, its AFM as my stock AFM is maxed out.
Tuning should fix your problem.