I have this issue on my laptop, but on my computer everything works normally, the thing is my computer use grapich cards resolution and my laptop is 1024x600, so I can tell almost for sure, the problem is the resolution of your computer with the skin, I really think that this skin should be opitional(on launcher), -I tryed to add it before the update and couldn't-, BUT.
I'm almost sure that if you delete the "Skin" folder on your YGOpro it will be like it was before the update and will work normally, just make sure to make a backup of the skin folder.
if you WANNA use the blue skin tough, you will probally need to re-adjust the resolution of the images or... somehow change your screen resolution.