Each tile in a CIV3 map has an associated continent number - generated by the Civ editor, note that bodies of water also count as continents. The continents are counted from the largest body of water to the smallest, then the largest land body to the smallest - so continent#0 is ususally the ocean.
The analysing tool just takes an array of tiles and sums the many tile attributes against continent nos (it keeps an array of the summed values so it dosent have to recount all the time).
IIRC MapTweaker dosen't modify continent nos when you move tiles about (and probably gives new tiles a continent no of 0 too...) fortunately this is one of the things that Civ3Edit will fix on loading.
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