I have the same Problem.
As suggested by the tech support site (https://mtgarena-support.wizards.com/hc/en-us/articles/360038694451-Display-Issues) I deleted the three entries in the registry. Now the game starts with the correct resolution (1680*1050). However as soon as I enter the Graphic Options Menu, the game reverts to a wrong resolution and I have to repeat the procedure.
I have the same Problem.
As suggested by the tech support site (https://mtgarena-support.wizards.com/hc/en-us/articles/360038694451-Display-Issues) I deleted the three entries in the registry. Now the game starts with the correct resolution (1680*1050). However as soon as I enter the Graphic Options Menu, the game reverts to a wrong resolution and I have to repeat the procedure.