There are no duplicates, one file is the normal airport AFCAD, the other one contains only approaches and both must be there and it's all normal. Tried just now, and I can see both the localizer and the glideslope correct and in sync with PAPIs when tuned to 110.90, see the attached screenshot.
The map also shows the ILS and the FSX gps does it too so, it must be something else.