How can I rasterize a spot color file without creating "border" pixels between areas that are adjacent to each other but should not be overlapping?

We use Illustrator to create circuit layouts. For part of our process, we create an image of all of the layers using spot colors to show the printed layers overlapping each other. We then rasterize the file and send the image through a Matlab routine that performs some analysis of the circuits based on the colors of the pixels.
In some cases, I have created images with areas next to each other, but not overlapping. When rasterizing the image, the rasterizing process appears to treat the borders as overlapping and creates a single pixel wide border between the 2 areas when there is none. This is playing havoc with our Matlab routine.
I can manually go in and remove the rasterized border, however on some projects, this is a very lengthy process. Has anyone experienced anything like this, or have any ideas on how to prevent this?

Would align to pixel grid help?
Left is not aligned, Right is aligned to pixel grid

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