For clarification, I know that you pick custom when you want special maps like Sotis or TD maps, and melee if you want good ol' RTS style. But why do we have to select "custom game" to earn achievements? why not melee?
This is confusing because there are two definitions for Custom in StarCraft II. There is the overarching Custom Game type which can have a Custom category or a Melee category.
Custom Game encompasses all games which are not one of the following:
You need to select Custom Game and the Melee category to earn achievements under the Custom Game achievement section. The reason for this is Melee category games always have the same conditions for victory--destroy all opponent buildings--whereas Custom category games can have any number of victory conditions, such as destroying the Nexus in Nexus Wars or defeating all waves of creeps in a Tower Defense game.