Like hows todays BGS patch notes might as well have said "Fixed some things"
(Sorry to be so negative, but my hat is particularly dirty. It will take some washing before it returns to its previously luminous white)
Fixed some negative faction consequences not being applied correctly from actions such as crimes and missions
My hope is that this bug has been the cause of the majority of the weirdness - no doubt further tweaking and squishing will be required but this change alone will help us properly identify further issues.
Its probably going to take weeks, but this is progress!