Do you use sub-forums or are all your forums listing on forum list? I seem to lose ground (post count) when using sub forums and I'm not a huge fan of them in the first place.
It really depends on the forum and what's most logical for your content. I use subforums on most forums because it makes logical sense to do it that way. Just make sure the subforums are displayed (not popups or dropdowns but displayed physically below the parent forums) so members can easily find them and they will get used.