There is no real logic to the ordering, other than that the top forum in each column is kind of the parent in that it's the most general of that area.
I personally think not ordering them based on post counts or age is a reasonably good thing as it reduces the chances of forums that're fairly inactive from being shoved right down at the bottom, consequently making them even harder to stumble upon. But then, putting those forums at the top would be daft too.
I don't think there's any problems with the ordering and I've not heard any complaints thus far. Plus, most people have the ordering built into their browsing habits so fiddling with them isn't something I fancy doing.
It's largely a case-by-case type thing.