Hi @raluaces,
I am facing the same issue. (you have explained the problem clearly in your post. For your reference, here is my discussion on this https://ttlc.intuit.com/community/state-taxes/discussion/re-california-non-residency-status-wrongly-... )
@TomD8atleast helped me fix some of the issue. After filling in correct info in Personal section of TT, atleast i am being treated as part-resident. In case u have not taken care of this and not filed yet, you can get this fixed.
Regarding the 540NR Schedule CA, line items 4 and 5 - the problem still remains for me...as you have pointed out before.
