You're not the only one reporting a problem with VA underpayment of ES-tax penalty.  @Babak also reported a similar issue last week but it's hard for us to figure out what exactly was wrong without seeing the actual calc: https://accountants.intuit.com/community/proconnect-tax-discussions/discussion/virginia-underpayment...

Definitely, there is something wrong with the programming of the 3Q payment.  The line with the wrong calculation is redundant and has the wrong day count.

@IntuitGabi Could you please have the programmers look into this and give us an update?  Thanks!