I am not sure that i have completely understood the differences in startup for the LTC2945 and the LTC2946. I have added code to reflect that there are two control registers but I am not sure i have configured these to match how the LTC2945 behaves on default.
Put simply, i was forced into using the 2946 as a replacement for the 2945 and don't need the extra features but want to make it work the same as it did.