If your house has gutters on the roof, and they are some distance away from the wall, then they form a sort of "umbrella" to stop rain running down the brickwork. Of course, if the wind blows, then rain can be pushed against the brickwork - generally the further down the house, the more is likely to be blown against the bricks.
Bricks are porous, but they're unlikely to pass water through them in any sort of quantity. What they will do is soak up water and hold on to it - that's more what you'd describe as "moisture" or "damp" and will quite happily rot woodwork (quite quickly) if it is in close proximity. There are paints and coatings to try to "seal up" brickwork to lessen their porousness, they have variable benefit though.
As identified, a double-skin of brick (with a gap between) allows any moisture or condensation on the outer skin to simply fall down the cavity to be drained away. On a single-skin brick wall, it's unlikely the inner surface of the bricks has been plastered and decorated into the room. It's more likely you have a layer of something (eg. stud wall or similar), which performs the same function as the inner layer of bricks in a double-skinned wall. In some situations, the outer bricks above a window have "weep holes" to let any water that may be pooling to dribble out.
If your windows frames are rotten, then they're most likely now even more porous than the brick - you can't paint over them to protect them, you'll need to replace the wood. You can (to some extent) do this by chipping out the obviously wet wood, drying the remainder (perhaps after a warm, sunny week) and then putting in filler. Once that's all hardened, paint it all thoroughly. In my experience, such a repair will likely only last a year or two - replacing the frames entirely is the "real" solution. When you do replace them, you can see if there's any sort of moisture barrier across the top of the frame - if there is, then it probably has holes in it, but it's there to stop the water getting into the frames, and hopefully would let water drain out of weep holes (if you have them, or will have them).
After all that, my guess is you have a leak somewhere you haven't yet found (bear in mind that water can find ways through gaps that are so small you may not be able to see them easily). My own experience has shown me that water can find its way from somewhere you think can't possibly be the source, and that just about every detail you disregard will eventually need addressing after several trial and error failures make you more and more desperate to find the cause.
You may also have moisture "pooling" in the top of the window frame (which may be mitigated by weep holes - although fixing the source is better than fixing the symptom). This may be the cause of the frame rotting more quickly than wind blown rain on its own would do.
You could use a damp meter to measure the moisture content of the bricks and wood. By doing this in the bad area and in a good one, you'll get an idea of the sorts of levels of moisture you can expect and should worry about. That doesn't solve anything directly, but it'll tell you if you've found the leak or not. You may also want to inspect the interior around the windows to make sure none of the moisture is coming inwards perhaps causing damp or other damage.
EDIT: As you've now added some pictures, whilst it's hard to tell, you have what I'd describe as "deep pointing". That is, there's a little space between the edge of the brick and the start of the pointing. There's nothing wrong with this, but it may mean that you have a little "shelf" for rain to accumulate on - and it then be able to seep through the pointing.
It's not a nice job, but after some rain, if things seem wetter than usual, then have a run around the pointing with the end of a screwdriver or something and see if there's any soft pointing. Don't hack away at it, but just see if there's any pointing that's a bit soft and comes away easily (ie. it's a bit like compacted wet sand). If there is, then it may be letting water through.
