JPG being a lossy format is why I was scanning to BMP then using Paint.net to save to JPG so I could edit the image without saving a lossy from a lossy. CanoScan Toolbox 4.6.1.2 only has BMP or JPG output support. I'll look into the PNG plugin.
According to Exif Pilot the XResolution and YResolution exif tags are set by Paint.net as they're not present in the original JPG image saved by the scanner.
The scanner -> JPG, re-saved by Paint.net -> JPG has "600/1" in both XResolution and YResolution exif tags
The scanner -> BMP, Save As by Paint.net -> JPG has "299999/500" in both XResolution and YResolution exif tags.
very odd.