I kept using it more and figured out how the bug triggers for me:
1) The colors indicated by the yellow arrows were not chosen by me. When I updated the script to the newest version those new color options appeared for me on the Advanced mode and started on those Hex codes you see.
2) I changed all of them. I saved the configuration and kept tweaking some colors I wasn't entirely convinced with. I know saving worked because, after choosing some colors I didn't like, I hit Load and it loaded everything I had before the recent changes, as intended.
3) This is when the bug triggers: When I finally choose the OK button, if I click on the Home tab, then back to the editor tab of my project and finally open the Theme Preferences window it opens up with the colors on the yellow arrows reset again. The theme doesn't change back unless I press the Apply button, though.
4) When I choose Load so I can use the custom configuration I had saved, it changes back all the colors except the ones pointed with the arrow.
So right now, the only way for me to keep all of the changes is to make them, apply them and then to ignore the Theme Preferences window since it will change back the next time I hit the Home tab and the saved configuration will not work for those new color options.
Hope this helps, I can make a video if necessary so let me know.