I know it's not very helpful (at least, not to me!), but I found that commenting the GRUB_GFXMODE option aligns the background image correctly. The reason this didn't help me much is that it
- caused loss of resolution to the background image
- changed the resolution and alignment of all other elements
- (worst of all) caused strange color issues with image elements where they grew darker while scrolling through the boot menu
This isn't the solution, but perhaps it's a step in the right direction?