I have a dualhead setup of 1600x1200 and 2560x1440 displays. I set a custom wallpaper image of 2560x1440px size, and set the scaling method to Zoom. Works as predicted. However when I log out and log back in, or reboot the machine, the larger display doesn't get the wallpaper applied at 1:1, but I do get a zoomed in version of it.

I suspect an issue in that there is a difference in how the system detected the order of the displays and the arrangement I have customized it (switched them).