I have the same problem.  Got the answer from the assistant:  Try input the HSA amount in State & Local/Modification/CA Modification field.  Check the CA Sch CA Column to see if the HSA amount doubled (one from W2 Box 12 input, one from State & Local input).  If it does, input minimum (rounding amount $1) in the State & Local input) so it won't affect Fed numbers.  I hope this helps.