This may simply be an issue with the comments on the generated ini files (no offense, but the plugin has several of those issues - possibly due to the comments being outdated?), please tell me what you think:

UnderWaterOre(Block,Size,Frequency,Rarity,maxDepth,BlockSource[,BlockSource2,BlockSource3.....])

Minimum parameters: 6

UnderWaterOre(SAND,7,4,100,DIRT,GRASS)
UnderWaterOre(CLAY,4,1,100,DIRT,CLAY)

Actual parameters: 5 each (plus one extra source for each)

I would hazard the maxDepth is missing?

Thanks for the report!