I have a modded install (1.12.2) with a few mods such as Snacks, Kerbal Construction Time, and Scrap Yard. I have stock planets and no physics-changing mods like FAR or RO. I have the strangest bug that occurs both in flight and in the VAB: Sometimes the dV tools assume that the mass of the entire stage is different from what it actually is (usually double). I figured out the root of the problem is to do with mass because "starting mass" is the thing that is obviously incorrect and it leads to incorrect TWR and dV calculations while Isp behaves as expected. I think the mass value is the issue because when the bug occurs in VAB, I can clearly see that the engineering report vessel mass and the first stage burn's starting mass are different (usually doubled). I am 99% sure it is only the displayed numbers that are wrong and the actual numbers are alright because I can take off with "0.6" TWR and reach LKO with "2000" dV. In VAB, removing and re-adding all the non-root parts fixes the issue by refreshing the calculation and in flight, reverting to launch sometimes corrects the issue.
I verify the game files frequently and there tends to be more than a few to reinstall each time, but even right after that the bug can occur. I think I'll install Kerbal Engineering Redux to compare values and maybe ignore stock calculations entirely but I wanted to post about this bug here too because I cannot believe no one has come across it before. Anyone?