Hi @Salk
I know what your talking about! The load behavior of a main menu load, a hard load (load game menu in game), an autosave load, and a quick load all have subtle but important differences.
This has actually come up in the speedrun world a few times. For example, the effect duration glitch (in which they last a long time) only happens if you have previously loaded a hard save in this session (as that messes up the global timers).
There's a variety of other small differences, between these functions; most of which I haven't dug too deeply into. But I'm unsurprised you've run into this before.
If you could provide an example of a specific script related issue that performs differently for different loads (to use as a reference point), I'd be happy to mount a bit of an investigation into it when I get the time. As mentioned above, it's a busy time of year so this may be backlogged a bit.
I'd also be happy to field any other questions!
Thanks, Lane