"as bob85 said, this is assuming a perfect ground. If the ground below the antenna is an imperfect ground, it will always add losses, and according to modeling, alot more than most people (including you by the numbers you have posted int he past) actually realize. Of course many people who model use the mininec ground, which has a nasty effect of over reporting the gain of ground mounted antennas to, actually, close to 6 dB. A recent image you posted that shows a 3/4 wavelength ground mounted antenna outperforming another antenna mounted higher has this problem..."
if anything the ground mounted vertical / monopole has been under reported from at least as far back as wolf (1966) & all that changed after 1997 with the logan rockway report that discovered the reality of the issue regarding the erroneous claim that stated that a dipole over ground has one half the effective area of a ground mounted monopole and that reality was that just the opposite has been, is and continues to be the case.
since logan and rockway wrote the original mininec program it doesn't surprise me that programs from somewhere past 1997 and on may have been updated at some point along the way with the appropriately adjusted algorithm. additional directivity is added to this initial 3 dB. depending on the adequacy of or number and length of the radials responsible for the collection of antenna current and presenting a high impedance to the shield to decouple the antenna current from the outside of the shield and connected support structures, a huge contribution to the elimination of loss resistance in the system, especially a problem as it applies to above ground vertical antennas making use of only 3 or 4 current collecting radials, wholly inadequate for the job at hand.
"the erroneous definition (postulated by Wolf, 1966) is that the effective area of the vertical receiving monopole is twice as large as that of a corresponding dipole in free space. this report shows that the effective area of a monopole is one half that of the corresponding dipole."
https://ia600105.us.archive.org/1/items/DTIC_ADA332891/DTIC_ADA332891.pdf
that's probably no error you're seeing, just a recent correction.
https://www.worldwidedx.com/threads/avanti-sigma4-an-alternative-view-point.31799/page-45#post-766894
