I thought that Adobe would have fixed this issue! I do not always delete images from my SD cards after importing them into my LR6 library. I also maintain an Aperture library for redundancy and experience no such issue as with LR6. When importing new images, and older ones are on the same SD card, LR6 in its infinite wisdom will rename the duplicate files with a -2. This first started whenever I shot raw and jpg together. It would rename only the jpg files. Now it does it to any file I import. I shoot with the Fuji X series and not entirely sure if this would apply to other makes/models of cameras. Just wish Adobe would fix this issue as not everyone will delete the files from their SD cards each time. (I suppose until there is a fix it is something that needs to be done.)
Absolutely. That is the first setting I verify before each import.
Next thing to try is to reset your LR Preferences as outlined here:
Instead of deleting the file rename it with .OLD extension: Lightroom 4 Preferences.agprefs.OLD If the issue isn't resolved you can delete the new Preferences file and remove the .OLD from the original file to restore it.
For got to add: LR should be closed when making the above changes to the Preferences file or restart it to load the new file.