So, I have done extensive tests on my end and I have failed to reproduce any of these bugs. Analysing the code, my suspicion is that your "new" save files for some reason have story flags from events that haven't happened yet set to true. Please make a backup of your save files, then delete them and start a new game to see if the problems persist.
The save files are store in C:\Users\%username\AppData\LocalLow\Necro Bunny Studios\Rise of the White Flower