If the POIs are truly duplicates (all information including latitude, longitude, name etc is identical), the unit will overwrite them and only use one. If it's really close -- like say two custom poi's that you have downloaded in different files, both for the same poi but the latitude and longitude are off by 0.0001, they will both show up. The only way to eliminate this is before you import the POI file to your machine -- delete the dups in a CSV file format.
As mentioned above, if ALL the information is duplicated, POILoader will overwrite and only one POI will be stored. If, however, the positioning data is close, but not exactly the same, multiple POI's will be atored.
totally agree with bgtee i had downloaded several times certain poi's after restarting my unit i found that i had multiple instances of the same poi with identical features, so i reckon that you should use the poi loader to remove previous custom poi's then disconnect from the PC ,reconnect then reload a new set of poi's , always backup your poi file to your PC and before adding any new poi's put them into your poi folder on your PC
remembering to remove the file before you update it so that you don't get ant duplicates.