Are you using any automatic fix or red-eye correction when importing. If so you will be creating an edited version.
Go to Edit >> Preferences >> Camera or Card Reader
Check your settings. Also check your import settings in the downloader by clicking on the Advanced dialog.
Please explain your workflow. Are your camera settingshave both raw and jpeg as image quality. This setting will produce two images of the same click, one with .jpeg extension and other in the raw format.