I'm seeing some pretty strange behavior with the atlas maker. I can manually tweak/fix the generated atlas afterward using photoshop and it fixes the problem, but it's still a bit odd and problematic.
I have a window that I'm drawing using 9 sprites (upper/mid/lower multiplied by left/center/right) with linear filtering turned off. All sprites have a semi transparent shadow in their "outer" facing pixels. The shadows look fine with the corner sections, but the shadows in the edge sections (which get stretched), always get baked in to the atlas with their transparency modified (they're about 2x more transparent).
It's definitely a problem with the atlas itself (rather than how it's displayed), since the pixels in the atlas image itself can be easily manually verified as being too transparent in an image editor. I've attached a screenshot that shows what the sections look like and red rectangles around the shadows that get effected. The shadows in the corner sections are not effected at all though. I don't think the source textures are the issue either, since they're what I use to manually fix the issue afterward... Unless it's a format incompatibility caused by photoshop saving those skinny sections differently.
I've also attached a screenshot of an atlas as generated by NGUI (before being manually fixed, but i did add red arrows to show where the issue occurs).
And I've attached a zoomed in example of the effect (top half is post-NGUI, bottom half is the source)