Ok, this has got me stumped. For some reason when importing images, they seem to be getting presets applied to them, even when not selected in the import process...what's going on?
When the images are first imported into Lightroom that embedded JPEG preview is first displayed while Lightroom generates a preview of the raw image data. The JPEG preview has adjustments applied by the camera that Lightroom doesn't read. Is this possibly what you are referring to?