Thank you for providing the diagnostic file. I reviewed the Form 5805 and related worksheets, the My Tax Data file, and the CA penalty interview entries using my Mac.
I agree that CA Form 5805 Part II Line 5 shows the same figure as Line 2, My Tax Data shows that Part II didn't contain any user entries; the user entries were in Part I.
I also saw that the amount appearing on the California Carryover Worksheet for the 2024 liability was a smaller figure than what appeared on Form 5805, Part II Line 5. As a result, I agree that the penalty calculated is higher than it would have been had the 2024 liability on the Carryover Worksheet been used for the comparison.
We will forward this issue for further investigation.
In the meantime, as it is getting close to the filing deadline, you could opt to leave the 5805 off the return and prepare a paper one separately to send to the FTB if you get a bill for the penalty that doesn't use the annualized method.
See here for contact information for the California FTB.
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