OK, so I've done some cursory testing to try to reproduce this issue. After investigating all the places that call the event (id = 10) that applies known_murderer and cross-referencing the differences in those which HIP overrides (only 1), I can't see a reasonable cause. However, it occurred to me that I've only technically seen this bug in HIP installs with VIET Events enabled. I've not seen it otherwise.
Thus, I installed HIP w/ no VIET Events and ran an observe for about 20 years. Manual inspection of rulers and their families (incl. children) hasn't revealed a single 'Known Murderer' modifier on any character.
Can somebody please try a HIP game without VIET Events installed (everything else default) and let me know whether they run into the 'Known Murderer' bug?
My theory is that something might be malformatted or typoed in the VIET Events 00_on_actions.txt. The ID '10' would be very easy to screw up like this in this type of file, which uses tons of '10 = <some other id>' style statements, where the 10 in that example is supposed to specify the random weight. However, a missing '=' or something of that matter might make the engine randomly call event 10 on characters, leading to this bug.
A little testing help would be appreciated, as it's time-consuming waiting for this bug to happen and locating it. But, hey, my quick test run w/o VIET Events seemed fine.