If I man not missinformed the region data on pgc in in most cases from Open street map and areas taged with admin_level=4 as the region data and Malta.
There was a tagging error on Manoel Island and the island was in two diffrent admin_level=4 Malta and "Manoel Island" This is probibly the reason that badegen says ther is 4 states in Malta but the maps region dialog only shows 3
Malta has no description what to tag as admin_level at http://wiki.openstreetmap.org/wiki/Tag:boundary%3Dadministrative
and no other admin_level tags exist except the one used at pgc, the wholy country and Sovereign Military Hospitaller Order of Saint John of Jerusalem of Rhodes and of Malta as a level 3
To add diffrent regions on PGC on polygondata had to exist and OSM has none.