AFAIK the POI's searched for include the Map you are using & Custom POI's.
If you removed the old map.img when updating then its POI's are removed with it as they are contained in the Map file itself.
I would think it more than likely that the duplicates on the Map you are seeing for those POI's would come down to Map Compilation data entry errors that have not been corrected by the Map makers, Sensis I believe.
New ones are added & subtracted in each map update, 4 updates a year.
They are not perfect by any means, on a recent trip to Sydney, I searched CN AU & NZ 2012.4 for Hospitals to find the quickest way to Royal North Shore Hospital, it wasn't even listed under Hospitals So I had to enter a nearby street address to get a rout to the area. I'm sure they will improve with time.
If you have been adding custom POI's from POI data bases then I guess duplicates are inevitable.
Hope that helps
Edit: Just looked on the Map using MapSource & the POI for The RNS Hospital is there, but it still isn't listed in the Find Places Under Hospitals
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