I am in the same boat, just received a letter from CA for 540NR for 16-17-18.  Based on the letter, it appears Proseries has been calculating the credit incorrectly.  I get that we are the accountants but, we pay a lot of $$$ for software that we must assume to a certain extent is calculating correctly.  It is not possible for a practitioner to know all 50 state income tax returns.  

Once I get the POA in with California, I will call California to discuss.  Then, escalate with Proseries.  My client has $5000 of interest due so there is a lot on the line.  

Question is if California has realized Proseries (Intuit) has made this error, then many Proseries returns will be looked at more.  

-leisa