The plugin authors say they have not done any changes recently so that must be from theme side.
What I notice weird on products where BOGO is enabled is that even after selecting variant, on cart page, it says it is not selected as in screenshot https://privatebin.support-tools.com/?31a893e70f14d98e#o+MwlCp0ajSOIR0k2XUWtnLvIXsPsZzlluloxkYbJao=
I can recall that I had submitted ticket here because I was not redirecting to the cart page automatically after add to cart button and from then my BOGO is not working, I guess. Can you have a look at it?