Let me re-type all of this since clicking submit without entering a title deletes the entire description...
Adding a keybind in User Prefs menu does not attach it to a key config profile. If you save the profile with the new keybinds they will be added to the profile but a second identical set will still exist independant of the profile. You can remove the unsaved duplicates by clicking the 'restore' button on the section to which they were added. If you don't do this, each time you save the profile another set of duplicate keybinds will be added to it.
To avoid this problem you can just make it check all new keybinds against the profile being saved and remove any duplicates.