I've been having this issue for a while now, and decided to stop playing it because of this bug. When I finally killed Jacob Seed, nothing out of the ordinary happened. When I checked the map his figure didn't show he was dead. I uninstalled, restarted, all sorts of stuff but couldn't fix it. I couldn't even go and kill Joseph.
Sorry if I didn't put a lot of information, been a while since I even got on.
Hi there, MeeperYeeter2! I'm sorry to hear about this. Would you be able to grab some video or screenshots exhibiting this issue? This would be incredibly helpful for me to have, so that I can investigate this further. Additionally, please try rebuilding your database to see if that helps! You can find the steps for that process here. It acts like a computer disk defragmenter and will not affect your save data, so it would be great to try to see if it helps get this corrected. Thanks!