It sounds like you are still fighting something, but your testing is depleting the CC so it doesn't show.

My first suggestion is shock the h*** out of the pool...Run your FC all the way up to 15ppm and keep it there for several days...that should solve your problem. Trying to keep it at 3 with a CYA of 40 is, IMHO, pushing your luck. For that CYA, 3 is the MINIMUM FC you can run.

So shock it up, hold it there for a few days, then try running your maintenance level at 6ppm and see if your chlorine usage goes down. I know, I know--use MORE bleach????? Yup, I suspect that is exactly what you need to do to solve your problem.

Good luck!