Ok, I figured out the issue through trial and error. It's caused by the Climate Trait! I'm used to using Endless Fields, so I went with that as the default for testing. When I turned off the trait, I immediately saw the issue.
My testing procedure was as follows:
As a general setup, unless otherwise stated: Map Size: Very Large: Geography Trait: Land, Clime Trait: Endless Fields, No Other Traits Counting only locations not associated with a free city after running the cheats to show the map and clear all breakable terrain; there are about 12 free cities per map.
Test 1: 4 liquid and 2 plants in the top quarter of the map. Four plants in the bottom three quarters of the map. Three liquid and six ore underground.
Test 2: 7 liquid in upper quarter, three plants in lower three quarters. Underground has 10 ore and five liquid.
Test 3 - Tropical Climate Trait: Three plants on surface, three liquids and nine ore underground.
Test 4 - Divide realm trait, Endless Fields climate. River running east to west; 7 liquids north of river, three plants south. Twelve ores and 3 liquids underground.
Test 5 - Land / Endless Fields + Explorative Underground: Five liquid in top quarter, three plants in bottom three quarters. One liquid and no ores underground.
Test 6 - Land / Endless Fields + No Free Cities + Explorative Underground: Six liquids and three plants in top third of map, seven plants in bottom third. One ore underground.
Test 7 - Land, No Climate Trait + No Free Cities: AHA! 15+ Liquids, 15+ Plants, 6 ores on surface. 4 liquids and 10+ ores underground.
Ok, so the climate traits for world generation need to be looked at. The Endless Fields one is particularly bugged; starting in the north of the map gives a much better start than the south as far as magic materials goes. You might also want to look at adding Magic Materials underground with the Explorative Underground trait.