I use a G600 mouse which allows you to map mouse clicks to the side buttons and this used to work and took a lot of strain off my hands when grinding long hours, but now any time I use the side buttons to do left or right clicks like I used to do the game just doesn't recognize it or simply ignores it.

Anyone else with this issue?

No but did you click the "Confirm" button or just "Ok"?  I have found you need to select confirm in most changes made to save them and ok is the same as cancel.  Which is weird.  I don't recall if there is a confirm button on keybindings or not, but always look around.

Hope you find a solution.

I don't have a G600, but a lefthanded Naga and don't have any problem with the sidebuttons.

How have you configured the buttons?
Which buttons/commands are assigned to the sidebuttons and where are they asigned to it (in BDO or the mouse software)?