I know of no new issues with Form 540-ES.
Since you are using a Desktop version, you could go to Forms mode and look at the completed Worksheet and Forms 54-ES. You can click inside a numeric field and click the magnifying glass to track the source of the entry. You can also use My Tax Data under Tools to look at all of the entries on the return and see which ones were entered by the user.
A direct payment can also be made to the state at any time.
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