Game version: 1.12.5
MechJeb2 version: 2.14.3.0 installed through CKAN

When you have long burns, the issue is the most noticeable. It seems like burn isn't split 50/50, but about 30/70. It isn't an auto-warp issue or craft rotating too slow. Happens no matter parts I use. Stock, ReStock, Cryo Engines, all have this.

I've seen people reporting similar issues back in 2014, but I use the latest version, so I am clueless. Is it known for some other mods to cause conflicts?

Long burns have to be done with a finite burn optimizer, not with the janky way the node executor currently interacts with KSP's infinite-impulse maneuver node implementation. This might get fixed at some point on the dev branch, but #1061 is the relevant issue and that has been open since 2018.

Also 50-50 isn't a rule, you need an optimizer to figure out the accurate split, 50-50 is just a close guess, but the deviation from 50-50 by the current node executor is likely very wrong anyway.

Oh, where can I find that finite burn optimizer? Is it part of MechJeb2 or it comes as separate mod?

Uh no, nothing like that exists in the KSP universe, one of the algorithms in the scientific literature needs to get implemented before anyone can use it.

Oh, well, bummer. Still, any recommendations what to do with maneuvers execution other than manual? Some kOS script or there is something more user friendly?

The version of the node executor in MJ-dev right now is the best of anything that I'm aware of in KSP

I know this issue is closed, but this definitely isn't right behaviour. The burn isn't even that long, under a minute. Either MJ node execution hates LHOX engines from Cryo Engines mod, or I'm missing something.