It's not the cause of your problem, but your hint brush usage could be tweaked some...
In the first pic, the hint brushes in the doorways are probably doing very little to help you out, as the bsp will automatically split up leaves here because of the brush placement. Try using area portals in instead, but make sure you cover ALL exits of the rooms, since each area MUST be enclosed by brushes (non-detail) or other area portals. Vertical hint brushes may do well with the hole in the ceiling, since it would allow the bsp to cull objects on the other side of the ceiling.
In the second pic, again, try area portals in the doorways. The bsp is already cutting the leaves for them, and area portals will cull more objects.
Your best use is probably in the third pic, since if you're in the hallway on the left, it will properly cull the room on the right. Good work.
On the last pic, instead of using vertical hint brushes, try a single horizontal one lined up with the top of the roof. This will allow the bsp to cull faces in the courtyard when you're standing outside the building, and vice versa.
Also, I'm not sure of this, but I think your arched doorways may be causing alot of extra leaves. Hint brushes on both sides of the doorways, or even making the arched parts of the doorways detail brushes would fix this (make a rectangular opening with regular brushes, and fill in the curved parts with detail brushes). It may or may not be a problem, it all depends on how the bsp interprets them.
Looking at your map in glview, or with mat_leafvis 1 can help you find ways of optimizing your map.