Can't Change Atlas Tree

When I go to Doriyani to move around some of my skill points in my atlas tree he just eats my gold and then the moment I load into a map it resets the skill tree to what it was before. I have made sure that they are all connected and yes I am pressing the confirm button. It even makes the sound and the little flash on all the nodes. Not sure what to do please help

I had a similar problem in version 0.1.1c.
When changing some points in the Atlas Tree, I noticed sometimes the confirmation wouldn't result in the exact skills I had chosen.

Also, when I picked a specific path, the tree would change it to something different, as show in the images here:
https://imgur.com/a/trO4Fy4

First image was what I wanted, but when changing areas, the path in the second image was selected.
After I refunded more nodes below those with problems, I was able to finally make the tree stay the way I wanted.