Hi Don,
You said, "also the culligan man said with this system i could just cut out the anode rod and it would be fine"...
I'm afraid to say that this is VERY BAD ADVICE, so you did good by replacing the anode rod. This advice will only lead to premature failure of your water heater...not advisable, for sure!!
Tell me, is softened water now feeding into the water heater? If so, then in my experience, this is causing your issue in and of itself! Here, softened water should feed the cold water to the house, but it should not feed the water heater...leads to issues with the anode rod.
Check out this link for more info.:
Hot water heater anodes and rust protection
I'm sure you can find more information if you google it, too!
Just FYI, OK?
Mark